From m.yavuz.18 at ogr.iu.edu.tr  Sun Feb  2 20:37:58 2020
From: m.yavuz.18 at ogr.iu.edu.tr (MUSTAFA YAVUZ)
Date: Sun, 2 Feb 2020 22:37:58 +0300
Subject: [FieldTrip] Data format transformation
In-Reply-To: <CAFrxm=xgGTsrA8bFRTikgf=WmAumC64GQ4VtpH5F5Z6m7bGi2g@mail.gmail.com>
References: <CAFWATv-hNBpy3a2fq0qrhU3gTXkJ__qby7qoRssxQj69J0JBHA@mail.gmail.com>
 <CAFrxm=xgGTsrA8bFRTikgf=WmAumC64GQ4VtpH5F5Z6m7bGi2g@mail.gmail.com>
Message-ID: <CAFWATv_1Jh5CJ1CvJJuq2NR2NMJ26NxCs4RhqjG268qRnGRSeQ@mail.gmail.com>

Dear Stephen,

Thank you so much for your help! After a little fight with the ft, it
worked out.

Stephen Whitmarsh <stephen.whitmarsh at gmail.com>, 28 Oca 2020 Sal, 19:33
tarihinde şunu yazdı:

> Hi Mustafa,
>
> That should be no problem; After you load the data in MATLAB, you can
> create your own 'raw' datastructure (explained here
> <http://www.fieldtriptoolbox.org/faq/how_are_the_various_data_structures_defined/>),
> and take it from there.
>
> Good luck,
> Stephen
>
> Op di 28 jan. 2020 om 14:27 schreef MUSTAFA YAVUZ <
> m.yavuz.18 at ogr.iu.edu.tr>:
>
>> Hi FT,
>>
>> I have EEG data with a non-conventional format which was segmented into
>> trials already and can be opened on MatLab. However, I want to preprocess
>> and analyse the data via Fieldtrip. On this point, I have trouble with cfg
>> structure and I can't utilize the information on the website. Hence, I
>> can't load and analyze the data on Fieldtrip. Is there anyone else who had
>> the same problem and find a solution?
>>
>> Thank you in advance,
>> Mustafa
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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From Joachim.Gross at glasgow.ac.uk  Mon Feb  3 11:21:07 2020
From: Joachim.Gross at glasgow.ac.uk (Joachim Gross)
Date: Mon, 3 Feb 2020 10:21:07 +0000
Subject: [FieldTrip] Faculty position at the University of Glasgow
Message-ID: <47487ADA-576C-4613-91FC-2ED3F48DD98A@glasgow.ac.uk>



The Centre of Cognitive Neuroimaging (CCNi) at the University of Glasgow is seeking to make a Professor/Reader/Senior Lecturer appointment.
The Centre brings together researchers developing and applying new Cognitive Neuroimaging Techniques and hosts a state-of-the art brain imaging facility (3T-fMRI, MEG/EEG, TMS/TES), with links to nearby 7T-fMRI. It is part of a multidisciplinary platform, crossing fundamental, social and cognitive neuroscience.
Applications are invited from candidates with an appropriate track record of academic achievement, and a track record in neuroimaging.
See https://www.jobs.ac.uk/job/BYJ278/professor-reader-senior-lecturer
Closing date: 2 March 2020 23:45
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From judy_tab95 at hotmail.com  Mon Feb  3 11:51:59 2020
From: judy_tab95 at hotmail.com (Judy Tabbal)
Date: Mon, 3 Feb 2020 10:51:59 +0000
Subject: [FieldTrip] AAL Parcellation on individual source model (HCP)
Message-ID: <DM6PR11MB4443D7978CFB88744B89547AE9000@DM6PR11MB4443.namprd11.prod.outlook.com>

Hello,

HCP provides in anatomy folder of each subject a sourcemodel.mat file with different resolution.
However, the corresponding coordinate system is in BTI. So, if I want to parcellate sources to AAL Atlas template provided in MNI coordinate system, how can I interpolate the individual sourcemodel to this atlas??
Because ft_sourceinterpolate requires that both are in the same coordinate system.

Thanks
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From jan.schoffelen at donders.ru.nl  Mon Feb  3 14:45:12 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Mon, 3 Feb 2020 13:45:12 +0000
Subject: [FieldTrip] AAL Parcellation on individual source model (HCP)
In-Reply-To: <DM6PR11MB4443D7978CFB88744B89547AE9000@DM6PR11MB4443.namprd11.prod.outlook.com>
References: <DM6PR11MB4443D7978CFB88744B89547AE9000@DM6PR11MB4443.namprd11.prod.outlook.com>
Message-ID: <21D3043E-1569-44A2-95FB-1DB5CEFBC2A7@donders.ru.nl>

Hi Judy,

The suggestion in this case would be to use the dipole location coordinates of the relevant standard_sourcemodel3d from the megconnectome/template (or fieldtrip/template/sourcemodel) directory.

Best wishes,
Jan-Mathijs

On 3 Feb 2020, at 11:51, Judy Tabbal <judy_tab95 at hotmail.com<mailto:judy_tab95 at hotmail.com>> wrote:

Hello,

HCP provides in anatomy folder of each subject a sourcemodel.mat file with different resolution.
However, the corresponding coordinate system is in BTI. So, if I want to parcellate sources to AAL Atlas template provided in MNI coordinate system, how can I interpolate the individual sourcemodel to this atlas??
Because ft_sourceinterpolate requires that both are in the same coordinate system.

Thanks
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

J.M.Schoffelen, MD PhD
Associate PI, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



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From s.caffarra at bcbl.eu  Tue Feb  4 19:55:37 2020
From: s.caffarra at bcbl.eu (Sendy Caffarra)
Date: Tue, 4 Feb 2020 19:55:37 +0100 (CET)
Subject: [FieldTrip] MEX file error
Message-ID: <1287202571.299715.1580842537849.JavaMail.zimbra@bcbl.eu>

Hi all,

I'm trying to use the latest version of Fieldtrip on Matlab R2019b (and MacOS Catalina 10.15.3) but it gives me this error:

>> cfg            = [];
cfg.dataset    = 'test.edf';
cfg.continuous = 'yes';
cfg.channel    = 'all';
data           = ft_preprocessing(cfg);

Invalid MEX-file '/Users/caffarra/Documents/toolbox/fieldtrip-20200130/utilities/ft_getopt.mexmaci64':
dlopen(/Users/caffarra/Documents/toolbox/fieldtrip-20200130/utilities/ft_getopt.mexmaci64, 6): no suitable image
found.  Did find:
        /Users/caffarra/Documents/toolbox/fieldtrip-20200130/utilities/ft_getopt.mexmaci64: code signature in
        (/Users/caffarra/Documents/toolbox/fieldtrip-20200130/utilities/ft_getopt.mexmaci64) not valid for use in
        process using Library Validation: library load disallowed by system policy

I've tried to recompile all MEX files using either ft_compile_mex or from terminal (as suggested here http://www.fieldtriptoolbox.org/faq/matlab_complains_about_a_missing_or_invalid_mex_file_what_should_i_do/) but I get the same error.

Any suggestion is more than welcome.
Thanks!

Sendy Caffarra




From elshafeh at gmail.com  Wed Feb  5 09:34:45 2020
From: elshafeh at gmail.com (Hesham ElShafei)
Date: Wed, 5 Feb 2020 09:34:45 +0100
Subject: [FieldTrip] New example on computing and reporting effect sizes
Message-ID: <46D8ABF9-CB5B-4266-A991-C4DE373E5854@gmail.com>

Dear fieldtrip users,

In adherence to our commitment to open reproducible science, we have developed a new example script on computing and reporting effect sizes using fieldtrip (http://www.fieldtriptoolbox.org/example/effectsize/). 

This example follows the already existing tutorials on statistics on event related fields (http://www.fieldtriptoolbox.org/tutorial/eventrelatedstatistics/). Here, we discuss our approach, its shortcomings and how it could/should be applied to other datasets. 

We are looking forward to your input on how we could improve this!. 

Best,
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From craiggrichter at gmail.com  Wed Feb  5 12:43:55 2020
From: craiggrichter at gmail.com (Craig Richter)
Date: Wed, 5 Feb 2020 12:43:55 +0100
Subject: [FieldTrip] MEX file error (Sendy Caffarra)
Message-ID: <FA0BDF57-98D0-4C4B-AB7A-737BD7570281@gmail.com>

Hi Sendy,

This appears to arise due to a ‘feature’ of the new MacOS, as the try to turn our PCs into iPhones... Catalina is applying very deep security, so since it doesn’t ‘know’ this mex, i.e. it hasn’t been notarized by Apple, the OS will not allow the access to libraries, etc. that it needs, hence the problem. See the attached discussion of the issue. Towards the bottom, it is suggested that with the current Catalina release, authorization may be given manually. If anybody knows how to do this, perhaps this is the workaround, or otherwise I suppose some submission will need to be made to Apple, i.e. got through the notarization process. As a rule-of-thumb, I try to stay an OS or two behind the current Apple release since they seem to becoming increasingly damaging with their updates.

https://bugs.launchpad.net/gcc-arm-embedded/+bug/1832620

Best,

Craig





From s.caffarra at bcbl.eu  Wed Feb  5 16:49:31 2020
From: s.caffarra at bcbl.eu (Sendy Caffarra)
Date: Wed, 5 Feb 2020 16:49:31 +0100 (CET)
Subject: [FieldTrip] MEX file error (Sendy Caffarra)
In-Reply-To: <FA0BDF57-98D0-4C4B-AB7A-737BD7570281@gmail.com>
References: <FA0BDF57-98D0-4C4B-AB7A-737BD7570281@gmail.com>
Message-ID: <2096524568.343625.1580917771538.JavaMail.zimbra@bcbl.eu>

Thank you Craig,

I could fix it by updating Catalina, Xcode and allowing all Apps in the Security panel.

Best,
Sendy

Sendy Caffarra
BCBL Staff Scientist & Stanford Visiting Scholar
https://sites.google.com/view/sendycaffarra
http://www.bcbl.eu/people/staff/sendy-caffarra/

----- Original Message -----
From: "Craig Richter" <craiggrichter at gmail.com>
To: "fieldtrip" <fieldtrip at science.ru.nl>
Cc: "s caffarra" <s.caffarra at bcbl.eu>
Sent: Wednesday, February 5, 2020 3:43:55 AM
Subject: Re: MEX file error (Sendy Caffarra)

Hi Sendy,

This appears to arise due to a ‘feature’ of the new MacOS, as the try to turn our PCs into iPhones... Catalina is applying very deep security, so since it doesn’t ‘know’ this mex, i.e. it hasn’t been notarized by Apple, the OS will not allow the access to libraries, etc. that it needs, hence the problem. See the attached discussion of the issue. Towards the bottom, it is suggested that with the current Catalina release, authorization may be given manually. If anybody knows how to do this, perhaps this is the workaround, or otherwise I suppose some submission will need to be made to Apple, i.e. got through the notarization process. As a rule-of-thumb, I try to stay an OS or two behind the current Apple release since they seem to becoming increasingly damaging with their updates.

https://bugs.launchpad.net/gcc-arm-embedded/+bug/1832620

Best,

Craig



From amine.jalal11 at gmail.com  Thu Feb  6 12:13:13 2020
From: amine.jalal11 at gmail.com (Amine JALAL)
Date: Thu, 6 Feb 2020 12:13:13 +0100
Subject: [FieldTrip] TFR : Common baseline for variable trial length
Message-ID: <CAPHS1+kmWMR_bm8WJCo4OEPc=OSRx7wanZ1pTRBed1MoqUpMfw@mail.gmail.com>

Dear Fieldtrippers,

I'm working on EEG data and I'm trying to perform a time-frequency
analysis. Since my data is continuous, I segmented it according to triggers
that define the trials (with variable length), so my data is composed by
the trials and two long segments at the beginning of the experiment
(resting state) and at the end.
My aim is to perform a baseline correction to the trials in TFR by taking
the baseline from the "resting state" segment.
I have been looking for the solution in the tutorials and mailing list, but
I didn't get to move forward.

I would be very grateful by any help or advice.
Thank you in advance.

Best,
Amine

-- 
*   Amine JALAL*
MD - Medical imaging & Instrumentation
Tél : +33 (0) 6 31 75 23 87
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From puszta.andris at gmail.com  Thu Feb  6 13:04:27 2020
From: puszta.andris at gmail.com (=?UTF-8?Q?Andr=C3=A1s_Puszta?=)
Date: Thu, 6 Feb 2020 13:04:27 +0100
Subject: [FieldTrip] TFR : Common baseline for variable trial length
In-Reply-To: <CAPHS1+kmWMR_bm8WJCo4OEPc=OSRx7wanZ1pTRBed1MoqUpMfw@mail.gmail.com>
References: <CAPHS1+kmWMR_bm8WJCo4OEPc=OSRx7wanZ1pTRBed1MoqUpMfw@mail.gmail.com>
Message-ID: <CAH-KfLzPYC5WhbczE8TjQT4SXRNpeprzR4S0dq+7k_wMyuPbDQ@mail.gmail.com>

Hi Amine,

I think you should be aware of 2 things:
1. "Trial number" of baseline matches with the trial number of the other
condition that you compare.
2. The selected baseline-period is in the original baseline-distribution's
CI

What I suggest is to cut randomly as many segments from the baseline as the
number of trials in the other condition, and as long segments as the length
of the trials. Next, check if the cutted baseline-segments are within the
original baseline's CI (for example by bootstrap resampling). After that
you can perform permutation statistics between baseline and the othe
condition, or normalize the condition and do permutation test against zero.

Hope I helped,

Andras

Amine JALAL <amine.jalal11 at gmail.com> ezt írta (időpont: 2020. febr. 6.,
Cs, 12:27):

> Dear Fieldtrippers,
>
> I'm working on EEG data and I'm trying to perform a time-frequency
> analysis. Since my data is continuous, I segmented it according to triggers
> that define the trials (with variable length), so my data is composed by
> the trials and two long segments at the beginning of the experiment
> (resting state) and at the end.
> My aim is to perform a baseline correction to the trials in TFR by taking
> the baseline from the "resting state" segment.
> I have been looking for the solution in the tutorials and mailing list,
> but I didn't get to move forward.
>
> I would be very grateful by any help or advice.
> Thank you in advance.
>
> Best,
> Amine
>
> --
> *   Amine JALAL*
> MD - Medical imaging & Instrumentation
> Tél : +33 (0) 6 31 75 23 87
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>


-- 
András Puszta MD, PhD
Helgeland Hospital / Univerity of Oslo
Department of Neuropsychology
Skjervengan 17 8657 Mosjøen, Norway
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From patrick.reisinger at stud.sbg.ac.at  Thu Feb  6 16:44:50 2020
From: patrick.reisinger at stud.sbg.ac.at (Patrick Reisinger)
Date: Thu, 6 Feb 2020 16:44:50 +0100
Subject: [FieldTrip] Salzburg Mind/Brain Annual meeting (July 16 & 17,
 2020) - Registration is open!
Message-ID: <d9038bec-187c-7240-54bd-2bf23ffc5ca2@stud.sbg.ac.at>

Dear all,

we are happy to announce that the 4th version of the Salzburg Mind Brain 
Annual Meeting (short SAMBA) is taking place from 16th to 17th of July 
2020 at the Faculty of Natural Sciences in Salzburg, Austria.

Our program includes the following great speakers:

- Olivier Collignon (University of Louvain)
- Philip Corlett (Yale University)
- Birte Forstmann (University of Amsterdam)
- Antonia Hamilton (University College London)
- Molly Henry (Max Planck Institute for Empirical Aesthetics)
- Janneke Jehee (Radboud University)
- Jean-Rémi King (Facebook AI, CNRS)
- Pieter Medendorp (Radboud University)
- Lucia Melloni (Max Planck Institute for Empirical Aesthetics)
- Hans Op de Beeck (KU Leuven)

Abstract deadline is on the 1st of April, registration deadline is on 
the 1st of May. Register soon under: https://samba.ccns.sbg.ac.at/

Any questions? Write an email to samba at sbg.ac.at.

We are looking forward to welcoming you to the city of Mozart!

All the best,

Your SAMBA organization team

-- 

Patrick Reisinger, MSc

PhD student at the Salzburg Brain Dynamics Lab 
(https://braindynamics.sbg.ac.at)

E-Mail: patrick.reisinger at sbg.ac.at
Phone: +43 662 8044 5161

University of Salzburg
Centre for Cognitive Neuroscience
Hellbrunner Straße 34
5020 Salzburg
Austria

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From parkerjo at stanford.edu  Fri Feb  7 00:33:08 2020
From: parkerjo at stanford.edu (Jonathon James Parker)
Date: Thu, 6 Feb 2020 23:33:08 +0000
Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing Workflow on PC
Message-ID: <BYAPR02MB575043282E5EC812196B677CAD1D0@BYAPR02MB5750.namprd02.prod.outlook.com>

Dear Fieldtrippers:

I am working to setup my imaging analysis pipeline to co-localize my SEEG electrodes from CT with patient-specific MRIs.

I am running fieldtrip August 2019 Build with Matlab 2017a on a Windows 10 machine. I am running into some errors which I suspect are due to the freesurfer dependency.

When I run ft_hastoolbox(‘freesurfer’) it returns 1, which I don’t quite understand as I thought freesurfer was only Mac/Linux? When I look in my fieldtrip external directory there is a freesurfer folder with some matlab files in there.

Are you aware of any work-arounds that will allow me to process the CT/MR images still using fieldtrip?

The specific files I am processing are nii.gz (indentified by field trip as nifti_fsl)

When I call ft_read_mri() I get the following results:
-----
Uncompressing stan2_ct.nii.gz to /tmp/tmp2696491.nii
The system cannot find the path specified.
ERROR: could not read /tmp/tmp2696491.nii
'rm' is not recognized as an internal or external command,
operable program or batch file.
ERROR: loading stan2_ct.nii.gz as analyze
Struct contents reference from a non-struct array object.

Error in ft_read_mri (line 396)
    ndims = numel(size(tmp.vol));

Error in jpImagingPipeline (line 12)
ct = ft_read_mri(ct_filename);


Thanks in advance!

Jonathon J. Parker MD, PhD
Resident in Neurosurgery
Morgridge Endowed Postdoctoral Fellow
Maternal & Child Health Research Institute
Department of Neurosurgery
Stanford University
E: parkerjo at stanford.edu<mailto:parkerjo at stanford.edu>


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From jan.schoffelen at donders.ru.nl  Fri Feb  7 09:35:23 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 7 Feb 2020 08:35:23 +0000
Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing Workflow
 on PC
In-Reply-To: <BYAPR02MB575043282E5EC812196B677CAD1D0@BYAPR02MB5750.namprd02.prod.outlook.com>
References: <BYAPR02MB575043282E5EC812196B677CAD1D0@BYAPR02MB5750.namprd02.prod.outlook.com>
Message-ID: <56E6D50D-81E1-464E-9256-221ABD935DDA@donders.ru.nl>

Dear Jonathon,

Indeed, Freesurfer typically used to run only on Linux/Mac. However, rumour has it that as of Windows 10 , freesurfer might run on Windows. For this you’d need to check out the Freesurfer documentation. If you need to run the Freesurfer recon-all pipeline to extract cortical meshes and/or a surface hull, you’d need to find out how to execute this processing step yourself.

With respect to the message you get from ft_hastoolbox: this refers to the availability (to matlab) of the relevant freesurfer code that uses Matlab (which are mainly functions related to loading Freesurfer specific file-formats into matlab for further processing). These functions in principle should work also on windows, with one possible exception, and that is the on-the-fly decompression of compressed anatomical images, which seems to be the problem that you are running into. I improved the Windows support for reading in zipped MR-images (*.nii.gz, and *.mgz) last December, and on my end it seems to work with a current version of the FieldTrip code. I should note, however, that I recently ran a training event, where several participants still did not manage to read in the zipped files on their own (Windows) laptops. This could have been due to their strange keyboard layouts (German/French/Asian etc.), but more likely this was the consequence of an interaction between Windows version, Matlab version and the students’ position in the room.

Long story short: could you upgrade to a more recent version of the Fieldtrip code (early January onwards to be safe), and check whether your problem persists?

Best wishes,

Jan-Mathijs

J.M.Schoffelen, MD PhD
Associate PI, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



On 7 Feb 2020, at 00:33, Jonathon James Parker <parkerjo at stanford.edu<mailto:parkerjo at stanford.edu>> wrote:

Dear Fieldtrippers:

I am working to setup my imaging analysis pipeline to co-localize my SEEG electrodes from CT with patient-specific MRIs.

I am running fieldtrip August 2019 Build with Matlab 2017a on a Windows 10 machine. I am running into some errors which I suspect are due to the freesurfer dependency.

When I run ft_hastoolbox(‘freesurfer’) it returns 1, which I don’t quite understand as I thought freesurfer was only Mac/Linux? When I look in my fieldtrip external directory there is a freesurfer folder with some matlab files in there.

Are you aware of any work-arounds that will allow me to process the CT/MR images still using fieldtrip?

The specific files I am processing are nii.gz (indentified by field trip as nifti_fsl)

When I call ft_read_mri() I get the following results:
-----
Uncompressing stan2_ct.nii.gz to /tmp/tmp2696491.nii
The system cannot find the path specified.
ERROR: could not read /tmp/tmp2696491.nii
'rm' is not recognized as an internal or external command,
operable program or batch file.
ERROR: loading stan2_ct.nii.gz as analyze
Struct contents reference from a non-struct array object.

Error in ft_read_mri (line 396)
    ndims = numel(size(tmp.vol));

Error in jpImagingPipeline (line 12)
ct = ft_read_mri(ct_filename);


Thanks in advance!

Jonathon J. Parker MD, PhD
Resident in Neurosurgery
Morgridge Endowed Postdoctoral Fellow
Maternal & Child Health Research Institute
Department of Neurosurgery
Stanford University
E: parkerjo at stanford.edu<mailto:parkerjo at stanford.edu>


_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202




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From amine.jalal11 at gmail.com  Fri Feb  7 10:00:32 2020
From: amine.jalal11 at gmail.com (Amine JALAL)
Date: Fri, 7 Feb 2020 10:00:32 +0100
Subject: [FieldTrip] TFR : Common baseline for variable trial length
In-Reply-To: <CAH-KfLzPYC5WhbczE8TjQT4SXRNpeprzR4S0dq+7k_wMyuPbDQ@mail.gmail.com>
References: <CAPHS1+kmWMR_bm8WJCo4OEPc=OSRx7wanZ1pTRBed1MoqUpMfw@mail.gmail.com>
 <CAH-KfLzPYC5WhbczE8TjQT4SXRNpeprzR4S0dq+7k_wMyuPbDQ@mail.gmail.com>
Message-ID: <CAPHS1+=WsFNiXT1iBtD=9zM3fP76+j3OwcQs2L5+nVjYxyrOVA@mail.gmail.com>

Hi Andras,

Thanks for reply and for your help.
I had roughly the same idea. It would be very useful.
Thank you once again.

Best,
Amine

Le jeu. 6 févr. 2020 à 13:35, András Puszta <puszta.andris at gmail.com> a
écrit :

> Hi Amine,
>
> I think you should be aware of 2 things:
> 1. "Trial number" of baseline matches with the trial number of the other
> condition that you compare.
> 2. The selected baseline-period is in the original baseline-distribution's
> CI
>
> What I suggest is to cut randomly as many segments from the baseline as
> the number of trials in the other condition, and as long segments as the
> length of the trials. Next, check if the cutted baseline-segments are
> within the original baseline's CI (for example by bootstrap resampling).
> After that you can perform permutation statistics between baseline and the
> othe condition, or normalize the condition and do permutation test against
> zero.
>
> Hope I helped,
>
> Andras
>
> Amine JALAL <amine.jalal11 at gmail.com> ezt írta (időpont: 2020. febr. 6.,
> Cs, 12:27):
>
>> Dear Fieldtrippers,
>>
>> I'm working on EEG data and I'm trying to perform a time-frequency
>> analysis. Since my data is continuous, I segmented it according to triggers
>> that define the trials (with variable length), so my data is composed by
>> the trials and two long segments at the beginning of the experiment
>> (resting state) and at the end.
>> My aim is to perform a baseline correction to the trials in TFR by taking
>> the baseline from the "resting state" segment.
>> I have been looking for the solution in the tutorials and mailing list,
>> but I didn't get to move forward.
>>
>> I would be very grateful by any help or advice.
>> Thank you in advance.
>>
>> Best,
>> Amine
>>
>> --
>> *   Amine JALAL*
>> MD - Medical imaging & Instrumentation
>> Tél : +33 (0) 6 31 75 23 87
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>>
>
>
> --
> András Puszta MD, PhD
> Helgeland Hospital / Univerity of Oslo
> Department of Neuropsychology
> Skjervengan 17 8657 Mosjøen, Norway
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>


-- 
*   Amine JALAL*
MD - Medical imaging & Instrumentation
Tél : +33 (0) 6 31 75 23 87
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From jan.schoffelen at donders.ru.nl  Fri Feb  7 13:46:43 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 7 Feb 2020 12:46:43 +0000
Subject: [FieldTrip] [hcp-users] Parcellate individual sourcemodel
In-Reply-To: <0bec6ea2-6c93-4650-9a04-d31bf1eee09a@humanconnectome.org>
References: <8743d089-12cf-493c-a153-30107f9ac836@humanconnectome.org>
 <09988C24-0199-45A9-A937-EC5CE5459E9D@gmail.com>
 <0bec6ea2-6c93-4650-9a04-d31bf1eee09a@humanconnectome.org>
Message-ID: <8F002B8A-5C90-47DA-9AB5-4B3AFFB40FC8@donders.ru.nl>

Hi Judy,

On 3 Feb 2020, at 15:03, Judy Tabbal <judytabal95 at gmail.com<mailto:judytabal95 at gmail.com>> wrote:

Thanks for your answer,
(1) okay so you mean i should use a template source model, then parcellate it to the atlas, then wrap it to individual space using subject specific mri, right?

Yes indeed. You can downsample the atlas to the template sourcemodel (provided they are in the same coordinate system).

(2) And another question concerning this, if i want to take advantage and use the individual source model provided in the anatomy subject: so after parcellating the template source model with AAL atlas, we can then detect the index of each ROI in the template grid position. Would these index be the same in the individual sourcemodel position as in the template sourcemodel position?

Indeed (and this also relate to the second part of your point (1)): the dipole positions in the individual sourcemodels have a 1-to-1 correspondence to the dipole positions in normalised space. Therefore, the atlas label that is attached to the template source positions directly applies to the individual sourcemodels as well. In other words, no warping is needed afterwards.

Note that you should either use the cfg.method = ‘mode’, or ’nearest’ if you will be using ft_sourceinterpolate to downsample the anatomical atlas.

Best wishes,
Jan-Mathijs


best regards,
Judy

On Monday, February 3, 2020 at 3:44:46 PM UTC+2, Jan Mathijs Schoffelen wrote:
Hi Judy,

The suggestion in this case would be to use the dipole location coordinates of the relevant standard_sourcemodel3d from the megconnectome/template (or fieldtrip/template/sourcemodel) directory.

Best wishes,
Jan-Mathijs


On 3 Feb 2020, at 14:20, Judy Tabbal <judyt... at gmail.com> wrote:

Hello,
i am bit confused with coordinate systems.
In fact, i want to parcellate the indivdual sourcemodel provided with anatomy folder (MEG HCP) for each subject using AAL Atlas.
However, AAL atlas is provided in MNI coordinate system and individual subject sourcemodel is in BTI system. So source interpolation will not work correctly with two different coord system.
What do you suggest in such case??
Thanks in advance

--
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To unsubscribe from this group and stop receiving emails from it, send an email to hcp-... at humanconnectome.org.
To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/8743d089-12cf-493c-a153-30107f9ac836%40humanconnectome.org<https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/8743d089-12cf-493c-a153-30107f9ac836%40humanconnectome.org?utm_medium=email&utm_source=footer>.


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From herrmann.b at gmail.com  Fri Feb  7 17:07:18 2020
From: herrmann.b at gmail.com (=?UTF-8?Q?Bj=C3=B6rn_Herrmann?=)
Date: Fri, 7 Feb 2020 11:07:18 -0500
Subject: [FieldTrip] Postdoc position in auditory cognitive neuroscience
Message-ID: <CAKzHZe45tQZnRLHhC+QOjp7O6qS+2NxRa=WcRZrRbfEDWjZMEw@mail.gmail.com>

Dear Fieldtrippers,

We are looking for a postdoctoral researcher who is excited about
auditory research. You would work with me in Toronto at the Rotman
Research Institute. Women, individuals w disabilities, Indigenous
people, POC & 2SLGBTQ+ individuals are encouraged to apply. Find
details on the application procedure at http://shorturl.at/beiEH.
Please forward to people you think could be interested.

Thank you,

Bjorn


----------
Björn Herrmann (PhD)

Scientist, Rotman Research Institute
Assistant Professor, Psychology, University of Toronto

email: herrmann.b at gmail.com
web: www.auditoryaging.com



From herrmann.b at gmail.com  Fri Feb  7 23:03:31 2020
From: herrmann.b at gmail.com (=?UTF-8?Q?Bj=C3=B6rn_Herrmann?=)
Date: Fri, 7 Feb 2020 17:03:31 -0500
Subject: [FieldTrip] Postdoc position in auditory cognitive neuroscience
Message-ID: <CAKzHZe4JGaY3ttp=3cXuRTsGz3ozdBL8xf6qLYCdsZrAFPocRw@mail.gmail.com>

Dear Fieldtrip colleagues,

My apologies for double posting, it seems that some people could not
open the link to the full job call in my previous post. Trying a new
one.

We are looking for a postdoctoral researcher who is excited about
auditory research. You would work with me in Toronto at the Rotman
Research Institute. Women, individuals w disabilities, Indigenous
people, POC & 2SLGBTQ+ individuals are encouraged to apply. Find
details on the application procedure at: http://tiny.cc/gzdqjz

Please forward to people you think could be interested.

Thank you,

Bjorn


----------
Björn Herrmann (PhD)

Scientist, Rotman Research Institute
Assistant Professor, Psychology, University of Toronto

email: herrmann.b at gmail.com
web: www.auditoryaging.com



From jiversen at ucsd.edu  Mon Feb 10 20:34:36 2020
From: jiversen at ucsd.edu (Iversen, John)
Date: Mon, 10 Feb 2020 19:34:36 +0000
Subject: [FieldTrip] Invitation to 4th International Mobile Brain/Body
 Imaging (MoBI) Conference this June in San Diego
Message-ID: <24CFB669-8D48-4A57-9EE1-1E43DD1055A3@ucsd.edu>

Dear Colleagues and Friends,

We are excited to invite you to San Diego for the 4TH INTERNATIONAL MOBILE BRAIN/BODY IMAGING (MoBI) CONFERENCE, which will take place *June 7-10, 2020* at the University of California San Diego hosted by the Swartz Center for Computational Neuroscience. 

* Abstract submission is now open (*Deadline March 6, 2020*) and discounted Early-Bird Registration is available through April 1st. Full conference information can be found at http://mobi2020.ucsd.edu.

Mobile Brain/Body Imaging (MoBI) is a maturing imaging approach employing mobile brain imaging methods synchronized to body motion capture and other behavioral and psychophysiological data streams to investigate brain dynamics accompanying natural cognitive and affective processes as humans interact with their environment and/or with others. MoBI2020 follows three highly successful conferences in Delmenhorst, Cancun and Berlin.

We hope you will join us for this dynamic meeting with enthusiastic MoBI researchers from all over the world and to enjoy the delights of San Diego in summertime. Sharing your ideas and projects with us will be a great opportunity for many researchers to learn and become even more motivated to work in this exciting field. The 2020 MoBI meeting will maintain the philosophy of the first meetings, where international leading experts in the field of MoBI will present ongoing research in different areas of MoBI.  We have three stimulating Keynotes planned by Stefan Debener (Benefits and pitfalls of wearable EEG), Laurel Trainor (Rhythm, prediction and multi-person interaction in music), and Sarah Robinson (Extended Organisms/Surrogate Bodies).  Oral sessions will include the latest developments in imaging hardware, new software solutions to record and analyze multi-modal data streams, and MoBI applications in a wide range of research areas including spatial cognition, motor control, gait rehabilitation, sport science, music and dance, therapeutic interventions and others.

We invite your submission for poster presentations that will allow for the opportunity to present and discuss your work. There will be ample time for informal interactions to foster transdisciplinary research ideas, provide the opportunity to learn about new perspectives and methods, and develop potential collaborative partnerships.

Students and Postdoctoral fellows are especially invited to apply, with discounted registration.

You can find more information about the conference, including venues, conference fees and a preliminary program here: http://mobi2020.ucsd.edu. Please visit for regular updates and announcements. In case you have questions or comments please contact John Iversen (jiversen at ucsd.edu).

Please circulate this announcement to colleagues and trainees. Our apologies if you have received multiple announcements through different lists.

We hope to welcome you in San Diego this June! 

With our best regards,

John Iversen and Klaus Gramman (Co-Chairs)


From mcfellner at gmail.com  Wed Feb 12 11:11:23 2020
From: mcfellner at gmail.com (Fellner, Marie-Christin)
Date: Wed, 12 Feb 2020 11:11:23 +0100
Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing,
 Workflow on PC
In-Reply-To: <mailman.5.1581073202.18228.fieldtrip@science.ru.nl>
References: <mailman.5.1581073202.18228.fieldtrip@science.ru.nl>
Message-ID: <272ffb3b-ffa1-a032-a998-5e2871b319cd@gmail.com>

Hi Jonathon,

I have run into similar problems of you with nii.gz files on a PC even 
with the most recent fieldtrip version.

The problem in my case was that the subfunction load_nifit.m used 
commands that did not run using the windows command line. Downloading 
and installing git (https://git-scm.com/) and crudely changing 
load_nifit.m helped for me.

I just replaced  "cmd = sprintf('zcat %s > %s', niftifile, 
new_niftifile);" to     "cmd = sprintf(' "C:\\Program 
Files\\Git\\bin\\bash.exe " zcat -c %s > %s', niftifile, new_niftifile);"

Further change all  "  unix(sprintf('rm -f %s', niftifile)); " to   
"delete(niftifile);"

Hope that helps!

Best,

Marie

Am 07.02.2020 um 12:00 schrieb fieldtrip-request at science.ru.nl:
> Message: 4
> Date: Thu, 6 Feb 2020 23:33:08 +0000
> From: Jonathon James Parker<parkerjo at stanford.edu>
> To:"fieldtrip at science.ru.nl"  <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing Workflow
> 	on PC
> Message-ID:
> 	<BYAPR02MB575043282E5EC812196B677CAD1D0 at BYAPR02MB5750.namprd02.prod.outlook.com>
> 	
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Fieldtrippers:
>
> I am working to setup my imaging analysis pipeline to co-localize my SEEG electrodes from CT with patient-specific MRIs.
>
> I am running fieldtrip August 2019 Build with Matlab 2017a on a Windows 10 machine. I am running into some errors which I suspect are due to the freesurfer dependency.
>
> When I run ft_hastoolbox(‘freesurfer’) it returns 1, which I don’t quite understand as I thought freesurfer was only Mac/Linux? When I look in my fieldtrip external directory there is a freesurfer folder with some matlab files in there.
>
> Are you aware of any work-arounds that will allow me to process the CT/MR images still using fieldtrip?
>
> The specific files I am processing are nii.gz (indentified by field trip as nifti_fsl)
>
> When I call ft_read_mri() I get the following results:
> -----
> Uncompressing stan2_ct.nii.gz to /tmp/tmp2696491.nii
> The system cannot find the path specified.
> ERROR: could not read /tmp/tmp2696491.nii
> 'rm' is not recognized as an internal or external command,
> operable program or batch file.
> ERROR: loading stan2_ct.nii.gz as analyze
> Struct contents reference from a non-struct array object.
>
> Error in ft_read_mri (line 396)
>      ndims = numel(size(tmp.vol));
>
> Error in jpImagingPipeline (line 12)
> ct = ft_read_mri(ct_filename);
>
>
> Thanks in advance!
>
> Jonathon J. Parker MD, PhD
> Resident in Neurosurgery
> Morgridge Endowed Postdoctoral Fellow
> Maternal & Child Health Research Institute
> Department of Neurosurgery
> Stanford University
> E:parkerjo at stanford.edu<mailto:parkerjo at stanford.edu>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:<http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200206/a0b682cd/attachment-0001.htm>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 7 Feb 2020 08:35:23 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)"<jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list<fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Problems with Fieldtrip MR/CT Processing
> 	Workflow on PC
> Message-ID:<56E6D50D-81E1-464E-9256-221ABD935DDA at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jonathon,
>
> Indeed, Freesurfer typically used to run only on Linux/Mac. However, rumour has it that as of Windows 10 , freesurfer might run on Windows. For this you’d need to check out the Freesurfer documentation. If you need to run the Freesurfer recon-all pipeline to extract cortical meshes and/or a surface hull, you’d need to find out how to execute this processing step yourself.
>
> With respect to the message you get from ft_hastoolbox: this refers to the availability (to matlab) of the relevant freesurfer code that uses Matlab (which are mainly functions related to loading Freesurfer specific file-formats into matlab for further processing). These functions in principle should work also on windows, with one possible exception, and that is the on-the-fly decompression of compressed anatomical images, which seems to be the problem that you are running into. I improved the Windows support for reading in zipped MR-images (*.nii.gz, and *.mgz) last December, and on my end it seems to work with a current version of the FieldTrip code. I should note, however, that I recently ran a training event, where several participants still did not manage to read in the zipped files on their own (Windows) laptops. This could have been due to their strange keyboard layouts (German/French/Asian etc.), but more likely this was the consequence of an interaction between Windows version, Matlab version and the students’ position in the room.
>
> Long story short: could you upgrade to a more recent version of the Fieldtrip code (early January onwards to be safe), and check whether your problem persists?
>
> Best wishes,
>
> Jan-Mathijs
>
> J.M.Schoffelen, MD PhD
> Associate PI, VIDI-fellow - PI, language in interaction
> Telephone: +31-24-3614793
> Physical location: room 00.028
> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands




From floss at apjanke.net  Wed Feb 12 12:28:15 2020
From: floss at apjanke.net (Andrew Janke)
Date: Wed, 12 Feb 2020 06:28:15 -0500
Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing,
 Workflow on PC
In-Reply-To: <272ffb3b-ffa1-a032-a998-5e2871b319cd@gmail.com>
References: <mailman.5.1581073202.18228.fieldtrip@science.ru.nl>
 <272ffb3b-ffa1-a032-a998-5e2871b319cd@gmail.com>
Message-ID: <fc54f068-a1c9-73d8-30d4-33c95806bd3e@apjanke.net>

What do y'all think about replacing these zcat calls with something
portable? Matlab has a gunzip() function, and the Java JRE that Matlab
ships with includes some gzip stuff in java.util.zip, so you could
accomplish this with native Matlab/Java code instead of calling out to
the system's zcat utility. I could write up a PR for this if you're
interested.

Or maybe I should send that PR directly to FreeSurfer instead of trying
to patch the copy that's included with FieldTrip?

Cheers,
Andrew

On 2/12/20 5:11 AM, Fellner, Marie-Christin wrote:
> Hi Jonathon,
>
> I have run into similar problems of you with nii.gz files on a PC even
> with the most recent fieldtrip version.
>
> The problem in my case was that the subfunction load_nifit.m used
> commands that did not run using the windows command line. Downloading
> and installing git (https://git-scm.com/) and crudely changing
> load_nifit.m helped for me.
>
> I just replaced  "cmd = sprintf('zcat %s > %s', niftifile,
> new_niftifile);" to     "cmd = sprintf(' "C:\\Program
> Files\\Git\\bin\\bash.exe " zcat -c %s > %s', niftifile, new_niftifile);"
>
> Further change all  "  unix(sprintf('rm -f %s', niftifile)); " to  
> "delete(niftifile);"
>
> Hope that helps!
>
> Best,
>
> Marie
>
> Am 07.02.2020 um 12:00 schrieb fieldtrip-request at science.ru.nl:
>> Message: 4
>> Date: Thu, 6 Feb 2020 23:33:08 +0000
>> From: Jonathon James Parker<parkerjo at stanford.edu>
>> To:"fieldtrip at science.ru.nl"  <fieldtrip at science.ru.nl>
>> Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing Workflow
>>     on PC
>> Message-ID:
>>     <BYAPR02MB575043282E5EC812196B677CAD1D0 at BYAPR02MB5750.namprd02.prod.outlook.com>
>>
>>     
>> Content-Type: text/plain; charset="windows-1252"
>>
>> Dear Fieldtrippers:
>>
>> I am working to setup my imaging analysis pipeline to co-localize my
>> SEEG electrodes from CT with patient-specific MRIs.
>>
>> I am running fieldtrip August 2019 Build with Matlab 2017a on a
>> Windows 10 machine. I am running into some errors which I suspect are
>> due to the freesurfer dependency.
>>
>> When I run ft_hastoolbox(‘freesurfer’) it returns 1, which I don’t
>> quite understand as I thought freesurfer was only Mac/Linux? When I
>> look in my fieldtrip external directory there is a freesurfer folder
>> with some matlab files in there.
>>
>> Are you aware of any work-arounds that will allow me to process the
>> CT/MR images still using fieldtrip?
>>
>> The specific files I am processing are nii.gz (indentified by field
>> trip as nifti_fsl)
>>
>> When I call ft_read_mri() I get the following results:
>> -----
>> Uncompressing stan2_ct.nii.gz to /tmp/tmp2696491.nii
>> The system cannot find the path specified.
>> ERROR: could not read /tmp/tmp2696491.nii
>> 'rm' is not recognized as an internal or external command,
>> operable program or batch file.
>> ERROR: loading stan2_ct.nii.gz as analyze
>> Struct contents reference from a non-struct array object.
>>
>> Error in ft_read_mri (line 396)
>>      ndims = numel(size(tmp.vol));
>>
>> Error in jpImagingPipeline (line 12)
>> ct = ft_read_mri(ct_filename);
>>
>>
>> Thanks in advance!
>>
>> Jonathon J. Parker MD, PhD
>> Resident in Neurosurgery
>> Morgridge Endowed Postdoctoral Fellow
>> Maternal & Child Health Research Institute
>> Department of Neurosurgery
>> Stanford University
>> E:parkerjo at stanford.edu<mailto:parkerjo at stanford.edu>
>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:<http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200206/a0b682cd/attachment-0001.htm>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Fri, 7 Feb 2020 08:35:23 +0000
>> From: "Schoffelen, J.M. (Jan Mathijs)"<jan.schoffelen at donders.ru.nl>
>> To: FieldTrip discussion list<fieldtrip at science.ru.nl>
>> Subject: Re: [FieldTrip] Problems with Fieldtrip MR/CT Processing
>>     Workflow on PC
>> Message-ID:<56E6D50D-81E1-464E-9256-221ABD935DDA at donders.ru.nl>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear Jonathon,
>>
>> Indeed, Freesurfer typically used to run only on Linux/Mac. However,
>> rumour has it that as of Windows 10 , freesurfer might run on
>> Windows. For this you’d need to check out the Freesurfer
>> documentation. If you need to run the Freesurfer recon-all pipeline
>> to extract cortical meshes and/or a surface hull, you’d need to find
>> out how to execute this processing step yourself.
>>
>> With respect to the message you get from ft_hastoolbox: this refers
>> to the availability (to matlab) of the relevant freesurfer code that
>> uses Matlab (which are mainly functions related to loading Freesurfer
>> specific file-formats into matlab for further processing). These
>> functions in principle should work also on windows, with one possible
>> exception, and that is the on-the-fly decompression of compressed
>> anatomical images, which seems to be the problem that you are running
>> into. I improved the Windows support for reading in zipped MR-images
>> (*.nii.gz, and *.mgz) last December, and on my end it seems to work
>> with a current version of the FieldTrip code. I should note, however,
>> that I recently ran a training event, where several participants
>> still did not manage to read in the zipped files on their own
>> (Windows) laptops. This could have been due to their strange keyboard
>> layouts (German/French/Asian etc.), but more likely this was the
>> consequence of an interaction between Windows version, Matlab version
>> and the students’ position in the room.
>>
>> Long story short: could you upgrade to a more recent version of the
>> Fieldtrip code (early January onwards to be safe), and check whether
>> your problem persists?
>>
>> Best wishes,
>>
>> Jan-Mathijs
>>
>> J.M.Schoffelen, MD PhD
>> Associate PI, VIDI-fellow - PI, language in interaction
>> Telephone: +31-24-3614793
>> Physical location: room 00.028
>> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202



From jan.schoffelen at donders.ru.nl  Wed Feb 12 13:24:33 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Wed, 12 Feb 2020 12:24:33 +0000
Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing,
 Workflow on PC
In-Reply-To: <fc54f068-a1c9-73d8-30d4-33c95806bd3e@apjanke.net>
References: <mailman.5.1581073202.18228.fieldtrip@science.ru.nl>
 <272ffb3b-ffa1-a032-a998-5e2871b319cd@gmail.com>
 <fc54f068-a1c9-73d8-30d4-33c95806bd3e@apjanke.net>
Message-ID: <96DA73A6-EA1A-47C3-84FE-2A3C27E28741@donders.ru.nl>

Dear Andrew and others,

Thanks for thinking along. In a recent version of the code, I thought I already addressed this issue. My solution was based on bypassing the section of freesurfer code that you refer to, because we now explicitly check whether a file is compressed (or a freesurfer_mgz image in combination with running the function on a PC), and decompess on-the-fly with gunzip, in ft_read_mri (around line 99 in ft_read_mri, using the private function inflate_file.m). A more principled solution could be indeed to fix it in load_nifti and PR to the freesurfer folks, and subsequently update our local copy that is shipped with FieldTrip. If it’s a clean fix, the freesurfer people typically acommodate such PRs, but the maintenance of their (often somewhat clunky) matlab code, does not seem to have priority. I suggest first that the Windows folks that have ran into problems recently update their FieldTrip version to one that is younger than December 2019 in order to check whether their problems persists, before taking any other action.

Best wishes,
Jan-Mathijs







> On 12 Feb 2020, at 12:28, Andrew Janke <floss at apjanke.net> wrote:
> 
> What do y'all think about replacing these zcat calls with something
> portable? Matlab has a gunzip() function, and the Java JRE that Matlab
> ships with includes some gzip stuff in java.util.zip, so you could
> accomplish this with native Matlab/Java code instead of calling out to
> the system's zcat utility. I could write up a PR for this if you're
> interested.
> 
> Or maybe I should send that PR directly to FreeSurfer instead of trying
> to patch the copy that's included with FieldTrip?
> 
> Cheers,
> Andrew
> 
> On 2/12/20 5:11 AM, Fellner, Marie-Christin wrote:
>> Hi Jonathon,
>> 
>> I have run into similar problems of you with nii.gz files on a PC even
>> with the most recent fieldtrip version.
>> 
>> The problem in my case was that the subfunction load_nifit.m used
>> commands that did not run using the windows command line. Downloading
>> and installing git (https://git-scm.com/) and crudely changing
>> load_nifit.m helped for me.
>> 
>> I just replaced  "cmd = sprintf('zcat %s > %s', niftifile,
>> new_niftifile);" to     "cmd = sprintf(' "C:\\Program
>> Files\\Git\\bin\\bash.exe " zcat -c %s > %s', niftifile, new_niftifile);"
>> 
>> Further change all  "  unix(sprintf('rm -f %s', niftifile)); " to  
>> "delete(niftifile);"
>> 
>> Hope that helps!
>> 
>> Best,
>> 
>> Marie
>> 
>> Am 07.02.2020 um 12:00 schrieb fieldtrip-request at science.ru.nl:
>>> Message: 4
>>> Date: Thu, 6 Feb 2020 23:33:08 +0000
>>> From: Jonathon James Parker<parkerjo at stanford.edu>
>>> To:"fieldtrip at science.ru.nl"  <fieldtrip at science.ru.nl>
>>> Subject: [FieldTrip] Problems with Fieldtrip MR/CT Processing Workflow
>>>     on PC
>>> Message-ID:
>>>     <BYAPR02MB575043282E5EC812196B677CAD1D0 at BYAPR02MB5750.namprd02.prod.outlook.com>
>>> 
>>>     
>>> Content-Type: text/plain; charset="windows-1252"
>>> 
>>> Dear Fieldtrippers:
>>> 
>>> I am working to setup my imaging analysis pipeline to co-localize my
>>> SEEG electrodes from CT with patient-specific MRIs.
>>> 
>>> I am running fieldtrip August 2019 Build with Matlab 2017a on a
>>> Windows 10 machine. I am running into some errors which I suspect are
>>> due to the freesurfer dependency.
>>> 
>>> When I run ft_hastoolbox(‘freesurfer’) it returns 1, which I don’t
>>> quite understand as I thought freesurfer was only Mac/Linux? When I
>>> look in my fieldtrip external directory there is a freesurfer folder
>>> with some matlab files in there.
>>> 
>>> Are you aware of any work-arounds that will allow me to process the
>>> CT/MR images still using fieldtrip?
>>> 
>>> The specific files I am processing are nii.gz (indentified by field
>>> trip as nifti_fsl)
>>> 
>>> When I call ft_read_mri() I get the following results:
>>> -----
>>> Uncompressing stan2_ct.nii.gz to /tmp/tmp2696491.nii
>>> The system cannot find the path specified.
>>> ERROR: could not read /tmp/tmp2696491.nii
>>> 'rm' is not recognized as an internal or external command,
>>> operable program or batch file.
>>> ERROR: loading stan2_ct.nii.gz as analyze
>>> Struct contents reference from a non-struct array object.
>>> 
>>> Error in ft_read_mri (line 396)
>>>      ndims = numel(size(tmp.vol));
>>> 
>>> Error in jpImagingPipeline (line 12)
>>> ct = ft_read_mri(ct_filename);
>>> 
>>> 
>>> Thanks in advance!
>>> 
>>> Jonathon J. Parker MD, PhD
>>> Resident in Neurosurgery
>>> Morgridge Endowed Postdoctoral Fellow
>>> Maternal & Child Health Research Institute
>>> Department of Neurosurgery
>>> Stanford University
>>> E:parkerjo at stanford.edu<mailto:parkerjo at stanford.edu>
>>> 
>>> 
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>>> 
>>> 
>>> ------------------------------
>>> 
>>> Message: 5
>>> Date: Fri, 7 Feb 2020 08:35:23 +0000
>>> From: "Schoffelen, J.M. (Jan Mathijs)"<jan.schoffelen at donders.ru.nl>
>>> To: FieldTrip discussion list<fieldtrip at science.ru.nl>
>>> Subject: Re: [FieldTrip] Problems with Fieldtrip MR/CT Processing
>>>     Workflow on PC
>>> Message-ID:<56E6D50D-81E1-464E-9256-221ABD935DDA at donders.ru.nl>
>>> Content-Type: text/plain; charset="utf-8"
>>> 
>>> Dear Jonathon,
>>> 
>>> Indeed, Freesurfer typically used to run only on Linux/Mac. However,
>>> rumour has it that as of Windows 10 , freesurfer might run on
>>> Windows. For this you’d need to check out the Freesurfer
>>> documentation. If you need to run the Freesurfer recon-all pipeline
>>> to extract cortical meshes and/or a surface hull, you’d need to find
>>> out how to execute this processing step yourself.
>>> 
>>> With respect to the message you get from ft_hastoolbox: this refers
>>> to the availability (to matlab) of the relevant freesurfer code that
>>> uses Matlab (which are mainly functions related to loading Freesurfer
>>> specific file-formats into matlab for further processing). These
>>> functions in principle should work also on windows, with one possible
>>> exception, and that is the on-the-fly decompression of compressed
>>> anatomical images, which seems to be the problem that you are running
>>> into. I improved the Windows support for reading in zipped MR-images
>>> (*.nii.gz, and *.mgz) last December, and on my end it seems to work
>>> with a current version of the FieldTrip code. I should note, however,
>>> that I recently ran a training event, where several participants
>>> still did not manage to read in the zipped files on their own
>>> (Windows) laptops. This could have been due to their strange keyboard
>>> layouts (German/French/Asian etc.), but more likely this was the
>>> consequence of an interaction between Windows version, Matlab version
>>> and the students’ position in the room.
>>> 
>>> Long story short: could you upgrade to a more recent version of the
>>> Fieldtrip code (early January onwards to be safe), and check whether
>>> your problem persists?
>>> 
>>> Best wishes,
>>> 
>>> Jan-Mathijs
>>> 
>>> J.M.Schoffelen, MD PhD
>>> Associate PI, VIDI-fellow - PI, language in interaction
>>> Telephone: +31-24-3614793
>>> Physical location: room 00.028
>>> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
> 
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202




From teddy.landron at gmail.com  Wed Feb 12 19:14:16 2020
From: teddy.landron at gmail.com (Ted Landron)
Date: Wed, 12 Feb 2020 19:14:16 +0100
Subject: [FieldTrip] [ft_databrowser] error: "left and right sides have a
 different number of elements"
Message-ID: <CAK7ge4du=DvLGM0ek0XhMVyeh2BZk3T5Ny+TQaL0hO9AGFk8vw@mail.gmail.com>

Dear fieldtrip community,

I'm Ted, PhD candidate at ICM, Paris.

I'm working on iEEG data, which I've preprocessed (bandpassed, mainly) and
have had it locked on the stimulus of interest & epoched (24 trials),
successfully so far.
However, when trying to visualise the epoched data using ft_databrowser,
matlab (not fieldtrip) raises an error. Here's how it looks like:

--------
ft_LFP_stimLock_iTask =

struct with fields:

           hdr: [1×1 struct]
         label: {6×1 cell}
          time: {1×24 cell}
         trial: {1×24 cell}
       fsample: 2048
    sampleinfo: [24×2 double]
           cfg: [1×1 struct]

--------

cfg                     = [];
cfg.channel       = 'all';
cfg.continuous   = 'no';
cfg.viewmode    = 'vertical';
cfg.allowoverlap = 'yes';
check_visu = ft_databrowser(cfg, ft_LFP_stimLock_iTask);

the input is raw data with 6 channels and 24 trials detected 0 visual
artifacts
the call to "ft_prepare_layout" took 0 seconds and required the additional
allocation of an estimated 0 MB
Unable to perform assignment because the left and right sides have a
different number of elements.

Error in ft_databrowser>redraw_cb (line 1811)
      eventtim(ievent) = (event(ievent).sample-begsample)/opt.fsample +
opt.hlim(1);

Error in ft_databrowser (line 733)
redraw_cb(h);
--------

I first tried to comment cfg entries one after the other but then resigned
myself to look for a similar bug on Google and the fieldtrip website, in
vain.
When "cfg.continuous  = 'yes';", it first seemed to work, but only for the
1.99 first seconds (~half the epoch length, stimulus locked at t = 2 s) as
the same error was raised when trying to visualise segments after 2 s.
I also cleared sampleinfo from the data structure ("clear
ft_LFP_stimLock_iTask.sampleinfo"), as suggested in one previous
ft_databrowser bug request but matlab keeps raising the same error.

Would any of you have an idea of how to fix this?

Many thanks,
-- 
*Ted Landron*

   - PhD candidate,
   Motivation Brain and Behavior (MBB
   <https://sites.google.com/site/motivationbrainbehavior/>) team,
   Institut du Cerveau et de la Moelle épinière (ICM
   <https://icm-institute.org/en/>), Sorbonne Université, Paris
   - Medical student, Université de Paris - Paris Descartes, Paris
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From acskwara at ucdavis.edu  Thu Feb 13 02:03:25 2020
From: acskwara at ucdavis.edu (Alea Skwara)
Date: Wed, 12 Feb 2020 17:03:25 -0800
Subject: [FieldTrip] Computing average power within a band following
 ft_freqanalysis
Message-ID: <CA+CcGtCCdk2mi1VUfw9qcvX=fzzBPC36_e0=K-PEU7f9__PhnA@mail.gmail.com>

Hi All,

I am doing an IAF-based analysis that requires me to extract average power
(or PSD) within frequency bands (e.g., alpha, beta) for subsequent
comparison. This means that I need an estimate in the form of a single
number for the whole range of frequencies subsumed within each frequency
band

My code when processing my data using ft_freqanalysis is as follows:

    cfg =[];
    cfg.method = 'mtmfft';
    cfg.output = 'pow';
    cfg.taper = 'hanning';
    cfg.channel = 'all';
    cfg.foilim = [lowerlim upperlim];   %of the band of interest
    cfg.trials = 'all';
    cfg.keeptrials = 'no';
    freq = ft_freqanalysis(cfg_band, data_segmented);

The resulting output is a struct containing a 2D matrix (powspctrm) with
the dimensions of 36 frequencies (in this case ranging from 12.5 to 30,
counting by .5) and 73 channels, with each cell containing a power estimate.

My questions are:
1) What are the units of what is contained in each cell, using the "pow"
output option? Are my units mV2 (power) or mV2/Hz (PSD)?

2) What is the most appropriate way to go from these frequency-wise
estimates to an estimate of band power (e.g., alpha power or beta power)?
If the units are in PSD, my understanding is that it would be appropriate
to take the simple mathematical average to calculate power within the band.
If they are in mV2, I am  unclear what the appropriate approach would be.
Using the bandpower function in matlab? Or does FieldTrip have a built in
function to calculate power within a band that I am somehow not finding?

Thanks in advance for your help,
Alea
-- 
Alea C. Skwara, M.A.
PhD Candidate | Saron Lab
http://saronlab.ucdavis.edu/

Center for Mind and Brain | University of California, Davis
267 Cousteau Place | Davis CA 95616
Cell: (828) 273-8595

Pronouns: She/Her/Hers
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From r.oostenveld at donders.ru.nl  Thu Feb 13 14:15:21 2020
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Thu, 13 Feb 2020 14:15:21 +0100
Subject: [FieldTrip] SAVE the date : CuttingEEG July 6-9 2020,
 Aix-en-Provence
References: <A3F4C5CF-CC4A-4708-A102-FBF6BDE4F6EA@univ-amu.fr>
Message-ID: <19ABDDF5-747E-4704-ACC1-B59D622A7741@donders.ru.nl>




Dear all,
 
We are excited to announce the 5th Symposium on Cutting edge methods for EEG research!!
 
Aix-en-Provence, July 6-9th
Before we finalize the program and open registrations, we wanted to make sure all those with interest can save the date!

Important points you should keep in mind:



This year, the conference will take place in the beautiful, charming and historical city of Aix-en-Provence <https://www.aixenprovencetourism.com/en/> from the 6th to the 9th of July 2020. The conference will be hosted by Aix-Marseille University in Le Cube <https://maps.app.goo.gl/Fui3gQXFvuUTQd7X7>, a brand-new venue hall. Note that we usually reach the waiting list in 4-5 days after the registration kick-off. To insure you don’t miss the opening make sure you are registered to the mailing list (by sending an empty email to  <>cuttingeeg-info-subscribe@ <mailto:cuttingeeg-info-subscribe at lists.hu-berlin.de>lists.hu-berlin.de <mailto:cuttingeeg-info-subscribe at lists.hu-berlin.de>)
 




This year CuttingEEG will inaugurate a new framework for the poster session to launch novel perspectives for participants, promote good practices and encourage open science. You will be able to register your abstract in one of three categories depending on the progression stage of your work (i.e. Planned study, In-progress study or Completed study). 



Note that the international festival of Lyrical art will take place in Aix-en-Provence at the same dates and will significantly affect the availability of accommodations. We have also reserved a limited number of single rooms in university dorms at 5 min walk from the venue which you may reserve upon request (at registration). These rooms will be available for a low price but are small (10m2) and offer a very basic comfort, do not hesitate to book your own accommodation if you prefer a higher level of comfort and additional options.
 


This year again, we will make efforts to limit as much as possible the conference carbon footprint. Therefore travels grants for journey with limited carbon footprint applications will be offered at registration.
Stay tuned, and most importantly, save the date!

The CuttingEEG organizing committee
Anne-Sophie Dubarry, Clément François & Maximilien Chaumon  



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From bkinkini at gmail.com  Thu Feb 13 14:43:24 2020
From: bkinkini at gmail.com (Kinkini .)
Date: Thu, 13 Feb 2020 14:43:24 +0100
Subject: [FieldTrip] ANT Neuro Channel Loc
Message-ID: <CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=okCZRCSUGw@mail.gmail.com>

Dear All,

I am a new member of this group and have started using fieldtrip very
recently.
I am using ANT Neuro wave guard 64-channel EEG cap for my study and I find
difficulty in figuring out the respective chan loc file. However I have
recently used 2D coordinates to prepare my own chan loc file, but its 90
degree rotated from clockwise.

Any information on this would be greatly appreciated.

Thanks and regards,

*Kinkini Bhadra*
*PhD Chandidate*
*Department of Fundamental Neuroscience*
*University of Geneva, Switzerland*
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From tzvetan.popov at uni-konstanz.de  Thu Feb 13 16:31:47 2020
From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov)
Date: Thu, 13 Feb 2020 16:31:47 +0100
Subject: [FieldTrip] ANT Neuro Channel Loc
In-Reply-To: <CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=okCZRCSUGw@mail.gmail.com>
References: <CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=okCZRCSUGw@mail.gmail.com>
Message-ID: <6123D479-9D89-4DFC-8A70-752222D1A556@uni-konstanz.de>

Dear Kinkini,

There is no channel location file unless you have digitized the electrodes yourself. I have attached a template electrode position of your system that I happened to use too. 
It can be used to compute neighbourhood struct for statistics or align to MNI template brain for source analysis.

You could use it to compute a layout file using ft_prepare_layout. Please type help ft_prepare_layout in the Matlab command window and evaluate the options. One of them, cfg.rotate is probably the cure for your 90 degree shift.
Wellcome the the FT list and good luck with your analyses
Tzvetan



> Am 13.02.2020 um 14:43 schrieb Kinkini . <bkinkini at gmail.com>:
> 
> Dear All,
> 
> I am a new member of this group and have started using fieldtrip very recently.
> I am using ANT Neuro wave guard 64-channel EEG cap for my study and I find difficulty in figuring out the respective chan loc file. However I have recently used 2D coordinates to prepare my own chan loc file, but its 90 degree rotated from clockwise. 
> 
> Any information on this would be greatly appreciated.
> 
> Thanks and regards,
> 
> Kinkini Bhadra
> PhD Chandidate
> Department of Fundamental Neuroscience
> University of Geneva, Switzerland
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202

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From tzvetan.popov at uni-konstanz.de  Thu Feb 13 16:36:21 2020
From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov)
Date: Thu, 13 Feb 2020 16:36:21 +0100
Subject: [FieldTrip] ANT Neuro Channel Loc
In-Reply-To: <CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=okCZRCSUGw@mail.gmail.com>
References: <CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=okCZRCSUGw@mail.gmail.com>
Message-ID: <39528459-5044-487C-AF2E-9D2C2E64A999@uni-konstanz.de>



From bkinkini at gmail.com  Thu Feb 13 21:17:00 2020
From: bkinkini at gmail.com (Kinkini .)
Date: Thu, 13 Feb 2020 21:17:00 +0100
Subject: [FieldTrip] ANT Neuro Channel Loc
In-Reply-To: <6123D479-9D89-4DFC-8A70-752222D1A556@uni-konstanz.de>
References: <CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=okCZRCSUGw@mail.gmail.com>
 <6123D479-9D89-4DFC-8A70-752222D1A556@uni-konstanz.de>
Message-ID: <CAM2-uk5uK=xtHbujWP9KM2V2QJZUnS=h8k-NqFPtMfzWQFk2AA@mail.gmail.com>

Hi  Tzvetan,

Thank you so much for your advice. Hopefully I will now be able to sort it
out.

Cheers,

Kinkini


On Thu, Feb 13, 2020 at 5:35 PM Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
wrote:

> Dear Kinkini,
>
> There is no channel location file unless you have digitized the electrodes
> yourself. I have attached a template electrode position of your system that
> I happened to use too.
> It can be used to compute neighbourhood struct for statistics or align to
> MNI template brain for source analysis.
>
> You could use it to compute a layout file using ft_prepare_layout. Please
> type *help ft_prepare_layout *in the Matlab command window and evaluate
> the options. One of them, cfg.rotate is probably the cure for your 90
> degree shift.
> Wellcome the the FT list and good luck with your analyses
> Tzvetan
>
>
>
> Am 13.02.2020 um 14:43 schrieb Kinkini . <bkinkini at gmail.com>:
>
> Dear All,
>
> I am a new member of this group and have started using fieldtrip very
> recently.
> I am using ANT Neuro wave guard 64-channel EEG cap for my study and I find
> difficulty in figuring out the respective chan loc file. However I have
> recently used 2D coordinates to prepare my own chan loc file, but its 90
> degree rotated from clockwise.
>
> Any information on this would be greatly appreciated.
>
> Thanks and regards,
>
> *Kinkini Bhadra*
> *PhD Chandidate*
> *Department of Fundamental Neuroscience*
> *University of Geneva, Switzerland*
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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From lmelloni at gmail.com  Fri Feb 14 09:09:26 2020
From: lmelloni at gmail.com (Lucia Melloni)
Date: Fri, 14 Feb 2020 09:09:26 +0100
Subject: [FieldTrip] Postdoctoral fellow for an international collaboration
Message-ID: <C9632763-8135-4FDE-BE8D-7B5E02469B2E@gmail.com>

Dear all,

There is an exciting opportunity for a 2-3 years senior post-doctoral research position to work with Michael Pitts at Reed College, Portland Oregon, USA (https://www.reed.edu/psychology/scalp/), and Liad Mudrik at Tel Aviv University, Tel Aviv, Israel (http://www.mudriklab.tau.ac.il) (location flexible in one of the two labs).

Project: International adversarial collaboration <https://science.sciencemag.org/content/366/6463/293?utm_campaign=toc_sci-mag_2019-10-17&et_rid=33778810&et_cid=3034188> on the neural basis of visual consciousness, aimed at testing key predictions of integrated information theory and global neuronal workspace theory. 
Collaborators include: Lucia Melloni, Stanislas Dehaene, Giulio Tononi, Christof Koch, David Chalmers, Hal Blumenfeld, Floris de Lange, Ole Jensen, Gabriel Kreiman, Huan Luo, Francis Fallon, and others.  

Required skills: 
•	expertise in advanced data analysis for as many of the following techniques as possible:EEG/MEG, fMRI, ECoG 
•	experience and interest in managing large datasets
•	experience and interest in cloud-based or local-cluster-based computing
•	interest and ability to work on team-based projects

Start date: Flexible between June and October 2020 
To apply: send an email including your  CV, research statement, and cover letter to mudrikli at tauex.tau.ac.il and mpitts at reed.edu by March 30th, 2020
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From Tineke.Grent at glasgow.ac.uk  Fri Feb 14 14:53:33 2020
From: Tineke.Grent at glasgow.ac.uk (Tineke Grent-'T-Jong)
Date: Fri, 14 Feb 2020 13:53:33 +0000
Subject: [FieldTrip] ANT Neuro Channel Loc
Message-ID: <LNXP265MB17554325D8D13E126462FBF1DC150@LNXP265MB1755.GBRP265.PROD.OUTLOOK.COM>

Dear Kinkini,

It's been a while since I have worked with ANT files, but if I remember correctly, the coordinates for the different electrodes are presented as Y-X-Z, rather than X-Y-Z locations in head-space (i.e. with respect to LPA, RPA, NAS). So try flipping the Y/X to X/Y columns and see whether this resolves the 90 degree rotation issue.

Best wishes,
Tineke Grent-'t-Jong


-----Original Message-----
From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of fieldtrip-request at science.ru.nl
Sent: 14 February 2020 12:00
To: fieldtrip at science.ru.nl
Subject: fieldtrip Digest, Vol 111, Issue 12

Send fieldtrip mailing list submissions to
	fieldtrip at science.ru.nl

To subscribe or unsubscribe via the World Wide Web, visit
	https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
or, via email, send a message with subject or body 'help' to
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When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..."


Today's Topics:

   1. ANT Neuro Channel Loc (Kinkini .)
   2. Re: ANT Neuro Channel Loc (Tzvetan Popov)
   3. Re: ANT Neuro Channel Loc (Tzvetan Popov)
   4. Re: ANT Neuro Channel Loc (Kinkini .)
   5. Postdoctoral fellow for an international collaboration
      (Lucia Melloni)


----------------------------------------------------------------------

Message: 1
Date: Thu, 13 Feb 2020 14:43:24 +0100
From: "Kinkini ." <bkinkini at gmail.com>
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] ANT Neuro Channel Loc
Message-ID:
	<CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=okCZRCSUGw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear All,

I am a new member of this group and have started using fieldtrip very recently.
I am using ANT Neuro wave guard 64-channel EEG cap for my study and I find difficulty in figuring out the respective chan loc file. However I have recently used 2D coordinates to prepare my own chan loc file, but its 90 degree rotated from clockwise.

Any information on this would be greatly appreciated.

Thanks and regards,

*Kinkini Bhadra*
*PhD Chandidate*
*Department of Fundamental Neuroscience* *University of Geneva, Switzerland*
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Message: 2
Date: Thu, 13 Feb 2020 16:31:47 +0100
From: Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] ANT Neuro Channel Loc
Message-ID: <6123D479-9D89-4DFC-8A70-752222D1A556 at uni-konstanz.de>
Content-Type: text/plain; charset="utf-8"

Dear Kinkini,

There is no channel location file unless you have digitized the electrodes yourself. I have attached a template electrode position of your system that I happened to use too. 
It can be used to compute neighbourhood struct for statistics or align to MNI template brain for source analysis.

You could use it to compute a layout file using ft_prepare_layout. Please type help ft_prepare_layout in the Matlab command window and evaluate the options. One of them, cfg.rotate is probably the cure for your 90 degree shift.
Wellcome the the FT list and good luck with your analyses Tzvetan



> Am 13.02.2020 um 14:43 schrieb Kinkini . <bkinkini at gmail.com>:
> 
> Dear All,
> 
> I am a new member of this group and have started using fieldtrip very recently.
> I am using ANT Neuro wave guard 64-channel EEG cap for my study and I find difficulty in figuring out the respective chan loc file. However I have recently used 2D coordinates to prepare my own chan loc file, but its 90 degree rotated from clockwise. 
> 
> Any information on this would be greatly appreciated.
> 
> Thanks and regards,
> 
> Kinkini Bhadra
> PhD Chandidate
> Department of Fundamental Neuroscience University of Geneva, 
> Switzerland _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202

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------------------------------

Message: 3
Date: Thu, 13 Feb 2020 16:36:21 +0100
From: Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] ANT Neuro Channel Loc
Message-ID: <39528459-5044-487C-AF2E-9D2C2E64A999 at uni-konstanz.de>
Content-Type: text/plain



------------------------------

Message: 4
Date: Thu, 13 Feb 2020 21:17:00 +0100
From: "Kinkini ." <bkinkini at gmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] ANT Neuro Channel Loc
Message-ID:
	<CAM2-uk5uK=xtHbujWP9KM2V2QJZUnS=h8k-NqFPtMfzWQFk2AA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi  Tzvetan,

Thank you so much for your advice. Hopefully I will now be able to sort it out.

Cheers,

Kinkini


On Thu, Feb 13, 2020 at 5:35 PM Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
wrote:

> Dear Kinkini,
>
> There is no channel location file unless you have digitized the 
> electrodes yourself. I have attached a template electrode position of 
> your system that I happened to use too.
> It can be used to compute neighbourhood struct for statistics or align 
> to MNI template brain for source analysis.
>
> You could use it to compute a layout file using ft_prepare_layout. 
> Please type *help ft_prepare_layout *in the Matlab command window and 
> evaluate the options. One of them, cfg.rotate is probably the cure for 
> your 90 degree shift.
> Wellcome the the FT list and good luck with your analyses Tzvetan
>
>
>
> Am 13.02.2020 um 14:43 schrieb Kinkini . <bkinkini at gmail.com>:
>
> Dear All,
>
> I am a new member of this group and have started using fieldtrip very 
> recently.
> I am using ANT Neuro wave guard 64-channel EEG cap for my study and I 
> find difficulty in figuring out the respective chan loc file. However 
> I have recently used 2D coordinates to prepare my own chan loc file, 
> but its 90 degree rotated from clockwise.
>
> Any information on this would be greatly appreciated.
>
> Thanks and regards,
>
> *Kinkini Bhadra*
> *PhD Chandidate*
> *Department of Fundamental Neuroscience* *University of Geneva, 
> Switzerland* _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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------------------------------

Message: 5
Date: Fri, 14 Feb 2020 09:09:26 +0100
From: Lucia Melloni <lmelloni at gmail.com>
To: undisclosed-recipients:;
Subject: [FieldTrip] Postdoctoral fellow for an international
	collaboration
Message-ID: <C9632763-8135-4FDE-BE8D-7B5E02469B2E at gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear all,

There is an exciting opportunity for a 2-3 years senior post-doctoral research position to work with Michael Pitts at Reed College, Portland Oregon, USA (https://www.reed.edu/psychology/scalp/), and Liad Mudrik at Tel Aviv University, Tel Aviv, Israel (http://www.mudriklab.tau.ac.il) (location flexible in one of the two labs).

Project: International adversarial collaboration <https://science.sciencemag.org/content/366/6463/293?utm_campaign=toc_sci-mag_2019-10-17&et_rid=33778810&et_cid=3034188> on the neural basis of visual consciousness, aimed at testing key predictions of integrated information theory and global neuronal workspace theory. 
Collaborators include: Lucia Melloni, Stanislas Dehaene, Giulio Tononi, Christof Koch, David Chalmers, Hal Blumenfeld, Floris de Lange, Ole Jensen, Gabriel Kreiman, Huan Luo, Francis Fallon, and others.  

Required skills: 
•	expertise in advanced data analysis for as many of the following techniques as possible:EEG/MEG, fMRI, ECoG 
•	experience and interest in managing large datasets
•	experience and interest in cloud-based or local-cluster-based computing
•	interest and ability to work on team-based projects

Start date: Flexible between June and October 2020 To apply: send an email including your  CV, research statement, and cover letter to mudrikli at tauex.tau.ac.il and mpitts at reed.edu by March 30th, 2020
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------------------------------

Subject: Digest Footer

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202


------------------------------

End of fieldtrip Digest, Vol 111, Issue 12
******************************************



From bkinkini at gmail.com  Mon Feb 17 00:26:03 2020
From: bkinkini at gmail.com (Kinkini .)
Date: Mon, 17 Feb 2020 00:26:03 +0100
Subject: [FieldTrip] ANT Neuro Channel Loc
In-Reply-To: <LNXP265MB17554325D8D13E126462FBF1DC150@LNXP265MB1755.GBRP265.PROD.OUTLOOK.COM>
References: <LNXP265MB17554325D8D13E126462FBF1DC150@LNXP265MB1755.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <CAM2-uk6gCkTChDwGG5z6CZFhcyfNhwJbT3shoVgE7-+BUP1o2A@mail.gmail.com>

Dear Tineke,

Thank you so much. Finally the chan loc file is working.
I did the XY swap as per your suggestion and it worked.

Thanks and regards,
*KINKINI BHADRA*


On Fri, Feb 14, 2020 at 2:54 PM Tineke Grent-'T-Jong <
Tineke.Grent at glasgow.ac.uk> wrote:

> Dear Kinkini,
>
> It's been a while since I have worked with ANT files, but if I remember
> correctly, the coordinates for the different electrodes are presented as
> Y-X-Z, rather than X-Y-Z locations in head-space (i.e. with respect to LPA,
> RPA, NAS). So try flipping the Y/X to X/Y columns and see whether this
> resolves the 90 degree rotation issue.
>
> Best wishes,
> Tineke Grent-'t-Jong
>
>
> -----Original Message-----
> From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of
> fieldtrip-request at science.ru.nl
> Sent: 14 February 2020 12:00
> To: fieldtrip at science.ru.nl
> Subject: fieldtrip Digest, Vol 111, Issue 12
>
> Send fieldtrip mailing list submissions to
>         fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>         fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
>         fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. ANT Neuro Channel Loc (Kinkini .)
>    2. Re: ANT Neuro Channel Loc (Tzvetan Popov)
>    3. Re: ANT Neuro Channel Loc (Tzvetan Popov)
>    4. Re: ANT Neuro Channel Loc (Kinkini .)
>    5. Postdoctoral fellow for an international collaboration
>       (Lucia Melloni)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Feb 2020 14:43:24 +0100
> From: "Kinkini ." <bkinkini at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] ANT Neuro Channel Loc
> Message-ID:
>         <CAM2-uk41KcHuEjgc8SQeLUbXhdNTp3Uhf9Ttq1O=
> okCZRCSUGw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All,
>
> I am a new member of this group and have started using fieldtrip very
> recently.
> I am using ANT Neuro wave guard 64-channel EEG cap for my study and I find
> difficulty in figuring out the respective chan loc file. However I have
> recently used 2D coordinates to prepare my own chan loc file, but its 90
> degree rotated from clockwise.
>
> Any information on this would be greatly appreciated.
>
> Thanks and regards,
>
> *Kinkini Bhadra*
> *PhD Chandidate*
> *Department of Fundamental Neuroscience* *University of Geneva,
> Switzerland*
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200213/0428c2ee/attachment-0001.htm
> >
>
> ------------------------------
>
> Message: 2
> Date: Thu, 13 Feb 2020 16:31:47 +0100
> From: Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] ANT Neuro Channel Loc
> Message-ID: <6123D479-9D89-4DFC-8A70-752222D1A556 at uni-konstanz.de>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Kinkini,
>
> There is no channel location file unless you have digitized the electrodes
> yourself. I have attached a template electrode position of your system that
> I happened to use too.
> It can be used to compute neighbourhood struct for statistics or align to
> MNI template brain for source analysis.
>
> You could use it to compute a layout file using ft_prepare_layout. Please
> type help ft_prepare_layout in the Matlab command window and evaluate the
> options. One of them, cfg.rotate is probably the cure for your 90 degree
> shift.
> Wellcome the the FT list and good luck with your analyses Tzvetan
>
>
>
> > Am 13.02.2020 um 14:43 schrieb Kinkini . <bkinkini at gmail.com>:
> >
> > Dear All,
> >
> > I am a new member of this group and have started using fieldtrip very
> recently.
> > I am using ANT Neuro wave guard 64-channel EEG cap for my study and I
> find difficulty in figuring out the respective chan loc file. However I
> have recently used 2D coordinates to prepare my own chan loc file, but its
> 90 degree rotated from clockwise.
> >
> > Any information on this would be greatly appreciated.
> >
> > Thanks and regards,
> >
> > Kinkini Bhadra
> > PhD Chandidate
> > Department of Fundamental Neuroscience University of Geneva,
> > Switzerland _______________________________________________
> > fieldtrip mailing list
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > https://doi.org/10.1371/journal.pcbi.1002202
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
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> >
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> >
>
> ------------------------------
>
> Message: 3
> Date: Thu, 13 Feb 2020 16:36:21 +0100
> From: Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] ANT Neuro Channel Loc
> Message-ID: <39528459-5044-487C-AF2E-9D2C2E64A999 at uni-konstanz.de>
> Content-Type: text/plain
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 13 Feb 2020 21:17:00 +0100
> From: "Kinkini ." <bkinkini at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] ANT Neuro Channel Loc
> Message-ID:
>         <CAM2-uk5uK=xtHbujWP9KM2V2QJZUnS=
> h8k-NqFPtMfzWQFk2AA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi  Tzvetan,
>
> Thank you so much for your advice. Hopefully I will now be able to sort it
> out.
>
> Cheers,
>
> Kinkini
>
>
> On Thu, Feb 13, 2020 at 5:35 PM Tzvetan Popov <
> tzvetan.popov at uni-konstanz.de>
> wrote:
>
> > Dear Kinkini,
> >
> > There is no channel location file unless you have digitized the
> > electrodes yourself. I have attached a template electrode position of
> > your system that I happened to use too.
> > It can be used to compute neighbourhood struct for statistics or align
> > to MNI template brain for source analysis.
> >
> > You could use it to compute a layout file using ft_prepare_layout.
> > Please type *help ft_prepare_layout *in the Matlab command window and
> > evaluate the options. One of them, cfg.rotate is probably the cure for
> > your 90 degree shift.
> > Wellcome the the FT list and good luck with your analyses Tzvetan
> >
> >
> >
> > Am 13.02.2020 um 14:43 schrieb Kinkini . <bkinkini at gmail.com>:
> >
> > Dear All,
> >
> > I am a new member of this group and have started using fieldtrip very
> > recently.
> > I am using ANT Neuro wave guard 64-channel EEG cap for my study and I
> > find difficulty in figuring out the respective chan loc file. However
> > I have recently used 2D coordinates to prepare my own chan loc file,
> > but its 90 degree rotated from clockwise.
> >
> > Any information on this would be greatly appreciated.
> >
> > Thanks and regards,
> >
> > *Kinkini Bhadra*
> > *PhD Chandidate*
> > *Department of Fundamental Neuroscience* *University of Geneva,
> > Switzerland* _______________________________________________
> > fieldtrip mailing list
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > https://doi.org/10.1371/journal.pcbi.1002202
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > https://doi.org/10.1371/journal.pcbi.1002202
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200213/7721cbef/attachment-0001.htm
> >
>
> ------------------------------
>
> Message: 5
> Date: Fri, 14 Feb 2020 09:09:26 +0100
> From: Lucia Melloni <lmelloni at gmail.com>
> To: undisclosed-recipients:;
> Subject: [FieldTrip] Postdoctoral fellow for an international
>         collaboration
> Message-ID: <C9632763-8135-4FDE-BE8D-7B5E02469B2E at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> There is an exciting opportunity for a 2-3 years senior post-doctoral
> research position to work with Michael Pitts at Reed College, Portland
> Oregon, USA (https://www.reed.edu/psychology/scalp/), and Liad Mudrik at
> Tel Aviv University, Tel Aviv, Israel (http://www.mudriklab.tau.ac.il)
> (location flexible in one of the two labs).
>
> Project: International adversarial collaboration <
> https://science.sciencemag.org/content/366/6463/293?utm_campaign=toc_sci-mag_2019-10-17&et_rid=33778810&et_cid=3034188>
> on the neural basis of visual consciousness, aimed at testing key
> predictions of integrated information theory and global neuronal workspace
> theory.
> Collaborators include: Lucia Melloni, Stanislas Dehaene, Giulio Tononi,
> Christof Koch, David Chalmers, Hal Blumenfeld, Floris de Lange, Ole Jensen,
> Gabriel Kreiman, Huan Luo, Francis Fallon, and others.
>
> Required skills:
> •       expertise in advanced data analysis for as many of the following
> techniques as possible:EEG/MEG, fMRI, ECoG
> •       experience and interest in managing large datasets
> •       experience and interest in cloud-based or local-cluster-based
> computing
> •       interest and ability to work on team-based projects
>
> Start date: Flexible between June and October 2020 To apply: send an email
> including your  CV, research statement, and cover letter to
> mudrikli at tauex.tau.ac.il and mpitts at reed.edu by March 30th, 2020
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200214/fa66171f/attachment-0001.htm
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> ------------------------------
>
> End of fieldtrip Digest, Vol 111, Issue 12
> ******************************************
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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From Anya_ml at wp.pl  Mon Feb 17 15:59:58 2020
From: Anya_ml at wp.pl (Anya_ml at wp.pl)
Date: Mon, 17 Feb 2020 15:59:58 +0100
Subject: [FieldTrip] Chile EEG workshop
Message-ID: <glx1y0-an8bwbwa6tv3-5oln99-u0i50qvquwcuna3aki-lzdjxv-fe7zf7-vs6cr-d42u4edbuatu69hje2f9p85v-t6rhktr6b0bhekso7l-srgnzn-5szivkfry748ere5eh-w5rreyzdb0sf121dex.1581951598265@email.android.com>

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From kris.de_meyer at kcl.ac.uk  Tue Feb 18 09:47:00 2020
From: kris.de_meyer at kcl.ac.uk (De Meyer, Kris)
Date: Tue, 18 Feb 2020 08:47:00 +0000
Subject: [FieldTrip] question about automatic artefact rejection
In-Reply-To: <AM0PR03MB60820E9A9469986E0E7DD87497160@AM0PR03MB6082.eurprd03.prod.outlook.com>
References: <AM0PR03MB60820E9A9469986E0E7DD87497160@AM0PR03MB6082.eurprd03.prod.outlook.com>
Message-ID: <AM0PR03MB6082896FB472BD7759940BA497110@AM0PR03MB6082.eurprd03.prod.outlook.com>

Dear Fieldtrippers,

In ft_artifact_muscle<http://www.fieldtriptoolbox.org/reference/ft_artifact_muscle>, an EEG signal is first filtered - usually with a bandpass filter with cutoff frequencies of [110,140]. The documentation then says that the hilbert envelope is calculated, after which the envelope values are z-transformed before they are thresholded.

However, is this sound? Whereas the actual filtered EEG values (the result of the bandpass filter) are usually normally distributed, the hilbert envelope values are far from.

What is the rationale for calculating the z-transform of a non-Gaussian distribution? Doesn't that introduce problems?

Best,

Kris





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From litvak.vladimir at gmail.com  Tue Feb 18 10:37:29 2020
From: litvak.vladimir at gmail.com (Vladimir Litvak)
Date: Tue, 18 Feb 2020 09:37:29 +0000
Subject: [FieldTrip] =?utf-8?q?PhD_studentship_=E2=80=93_Modelling_cortic?=
	=?utf-8?q?o-subcortical_oscillatory_connectivity=2E?=
In-Reply-To: <CACq1BhL_AcbHq9D0P5Yw3s5xOOwj0OBw4qNxdLKtWJ2==dCKsw@mail.gmail.com>
References: <CACq1BhL_AcbHq9D0P5Yw3s5xOOwj0OBw4qNxdLKtWJ2==dCKsw@mail.gmail.com>
Message-ID: <CACq1BhL+6VxPfP8FVV_Ho3c4fN6rFhLRShXougvEjQytfji9LA@mail.gmail.com>

*PhD Studentship – Modelling cortico-subcortical oscillatory connectivity.*



Applications are invited for a 3-year funded PhD studentship in the
Wellcome Centre for Human Neuroimaging (https://www.fil.ion.ucl.ac.uk/)
under the supervision of Dr. Vladimir Litvak and Dr. Simon Farmer and in
collaboration with the Computational Neuroscience Group (CNS,
https://www.upf.edu/web/cns), led by Prof. Gustavo Deco, at the Center for
Brain and Cognition (https://www.upf.edu/web/cbc), Pompeu Fabra University
(Barcelona, Spain).  The position is part of the EU-funded Innovative
Training Network euSNN (“European School of Network Neuroscience”) and
available, with full-time employment, for a duration of 3 years with
immediate start.



The euSNN Innovative Training Network integrates 16 leading European groups
in network neuroscience and 7 companies to train students who want to
pursue a successful career in the field of network neuroscience. The euSNN
training programme offers a unique combination of experimental, analysis
and modelling approaches. Exploiting intense collaborations between
experimental, theoretical and clinical groups, euSNN links basic research
on large-scale brain dynamics with new pathophysiological approaches and
clinical applications. The euSNN network is coordinated by Prof. Dr.
Andreas K. Engel. Further information on the euSNN network can be found at
http://eusnn.eu.



*Project details*



Deep Brain Stimulation (DBS) is an effective treatment method for a range
of neurological and psychiatric conditions. It involves placing electrodes
deep in a patient’s brain, usually in precisely targeted subcortical
nuclei. DBS surgery affords a unique opportunity to study the neural
activity of these nuclei via recording of local electrical signals known as
local field potentials (LFP). Our group pioneered simultaneous recording of
subcortical LFP with non-invasive whole brain imaging using
magnetoencephalography (MEG). This makes it possible to map out
cortico-subcortical oscillatory coherent networks which have characteristic
frequencies and cortical topographies for each subcortical target. Over the
years we collected data from several different subcortical nuclei and
characterised their oscillatory networks. The aim of the proposed project
is to establish a modelling framework which could accommodate these
findings and make quantitative predictions for future experiments. This
will require extending existing models of cortical dynamics and integrating
information from additional imaging modalities such as functional MRI and
Diffusion Tensor Modelling (DTI).



The euSNN training network offers exciting and unique opportunities for the
student to pursue this project including interactions with top experts in
neuroimaging brain modelling and exposure to several different modelling
frameworks and approaches that the student will have to master and
integrate to achieve the project’s goals. There might also be opportunities
towards the end of the project to test some of the predictions
experimentally. In addition, the student will have a chance to work on
secondments with commercial companies on topics relevant to the project.



*Funding notes*

The starting date can be any date between being offered the position and 1st
October 2020 and the contract is for 36 months. The studentship includes
UK/EU tuition fees and a stipend along with additional funds to cover
travel and accommodation during secondments and network activities.
Overseas fees cannot be covered.



*Entry requirements*

Applicants should have an Honours Degree (minimum 2:1) in a quantitative
discipline: Physics/ Mathematics/Engineering/Computer science, strong
mathematical background and interest in neuroscience. Knowledge of
scientific programming languages, particularly Matlab, background in
modelling complex physical systems and a relevant Masters qualification is
desirable. Applicants should be willing to travel to attend the network
activities and spend prolonged periods of time (up to a few months at a
time and at least 8 months in total) doing secondments outside the UK.
*Applicants
must not have been residing in the UK for more than 12 months prior to the
start of the appointment.*



*Deadline 30th April 2020. Shortlisted candidates will be interviewed in
May.*



*How to apply:*


Applicants should submit 1) a CV, 2) a 1-page statement detailing why you
want to do the PhD, motivation, interest and suitability for the project,
3) a copy of your strongest single piece of academic work (e.g. thesis,
publication), and 4) contact details of two referees. Please ensure that
each document is clearly labelled with your surname. Please send all
documents to Kamlyn Ramkissoon k.ramkissoon at ucl.ac.uk
<k.ramkissoon at ucl.ac.uk%20>by *30th April 2020*. Interviews will be held in
May 2020. Informal enquiries are welcome to Dr Vladimir Litvak (email:
v.litvak at ucl.ac.uk).
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From e.spaak at donders.ru.nl  Tue Feb 18 11:45:03 2020
From: e.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 18 Feb 2020 11:45:03 +0100
Subject: [FieldTrip] question about automatic artefact rejection
In-Reply-To: <AM0PR03MB6082896FB472BD7759940BA497110@AM0PR03MB6082.eurprd03.prod.outlook.com>
References: <AM0PR03MB60820E9A9469986E0E7DD87497160@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <AM0PR03MB6082896FB472BD7759940BA497110@AM0PR03MB6082.eurprd03.prod.outlook.com>
Message-ID: <CABPNLUp-+Baq4zTruv5bhH76B6tpQ3Tudk-4jJ-VBBnDW6Hcfg@mail.gmail.com>

Dear Kris,

Since there is no statistical test involved, I see no problems with
computing a z-score here. Think of it more as bringing the data into a
sensible range and allowing yourself to forget about details like
measurement unit etc. You could also not do the z-transform, and
simply specify a threshold based on raw amplitude, this would be
equivalent (but might make it potentially more difficult to come up
with a good threshold).

Best,
Eelke

On Tue, 18 Feb 2020 at 09:47, De Meyer, Kris <kris.de_meyer at kcl.ac.uk> wrote:
>
> Dear Fieldtrippers,
>
> In ft_artifact_muscle, an EEG signal is first filtered - usually with a bandpass filter with cutoff frequencies of [110,140]. The documentation then says that the hilbert envelope is calculated, after which the envelope values are z-transformed before they are thresholded.
>
> However, is this sound? Whereas the actual filtered EEG values (the result of the bandpass filter) are usually normally distributed, the hilbert envelope values are far from.
>
> What is the rationale for calculating the z-transform of a non-Gaussian distribution? Doesn't that introduce problems?
>
> Best,
>
> Kris
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202



From kris.de_meyer at kcl.ac.uk  Wed Feb 19 13:13:04 2020
From: kris.de_meyer at kcl.ac.uk (De Meyer, Kris)
Date: Wed, 19 Feb 2020 12:13:04 +0000
Subject: [FieldTrip] question about automatic artefact rejection
In-Reply-To: <CABPNLUp-+Baq4zTruv5bhH76B6tpQ3Tudk-4jJ-VBBnDW6Hcfg@mail.gmail.com>
References: <AM0PR03MB60820E9A9469986E0E7DD87497160@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <AM0PR03MB6082896FB472BD7759940BA497110@AM0PR03MB6082.eurprd03.prod.outlook.com>,
 <CABPNLUp-+Baq4zTruv5bhH76B6tpQ3Tudk-4jJ-VBBnDW6Hcfg@mail.gmail.com>
Message-ID: <AM0PR03MB60820BB9108F66ACB2892F6697100@AM0PR03MB6082.eurprd03.prod.outlook.com>

Thank you for your response, Eelke.

I guess it makes sense but it does make the selection of a threshold more arbitrary.

If your underlying distribution is normal, then a z-score of 3, 4 or 5 has a clear meaning in terms of outlier detection.

For a non-Gaussian distribution, that interpretation no longer holds, and rejection becomes less automated and more open to subjective interpretation.

Isn't it better to z-transform the Hilbert-envelope values with the mean/std or the median/mad of the original filtered EEG distribution rather than the mean/std or median/mad of the hilbert values distribution? That way, the meaning of the threshold magnitude would remain valid. Or is that what is happening in the code already?

Best,

Kris



________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Eelke Spaak <e.spaak at donders.ru.nl>
Sent: 18 February 2020 10:45
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] question about automatic artefact rejection

Dear Kris,

Since there is no statistical test involved, I see no problems with
computing a z-score here. Think of it more as bringing the data into a
sensible range and allowing yourself to forget about details like
measurement unit etc. You could also not do the z-transform, and
simply specify a threshold based on raw amplitude, this would be
equivalent (but might make it potentially more difficult to come up
with a good threshold).

Best,
Eelke

On Tue, 18 Feb 2020 at 09:47, De Meyer, Kris <kris.de_meyer at kcl.ac.uk> wrote:
>
> Dear Fieldtrippers,
>
> In ft_artifact_muscle, an EEG signal is first filtered - usually with a bandpass filter with cutoff frequencies of [110,140]. The documentation then says that the hilbert envelope is calculated, after which the envelope values are z-transformed before they are thresholded.
>
> However, is this sound? Whereas the actual filtered EEG values (the result of the bandpass filter) are usually normally distributed, the hilbert envelope values are far from.
>
> What is the rationale for calculating the z-transform of a non-Gaussian distribution? Doesn't that introduce problems?
>
> Best,
>
> Kris
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=miiXPIhNF0zd23xrFrXakUxAUldGY6DZLnhoajNtLlg%3D&amp;reserved=0
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0

_______________________________________________
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https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0
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From jan.schoffelen at donders.ru.nl  Wed Feb 19 13:25:22 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Wed, 19 Feb 2020 12:25:22 +0000
Subject: [FieldTrip] question about automatic artefact rejection
In-Reply-To: <AM0PR03MB60820BB9108F66ACB2892F6697100@AM0PR03MB6082.eurprd03.prod.outlook.com>
References: <AM0PR03MB60820E9A9469986E0E7DD87497160@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <AM0PR03MB6082896FB472BD7759940BA497110@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <CABPNLUp-+Baq4zTruv5bhH76B6tpQ3Tudk-4jJ-VBBnDW6Hcfg@mail.gmail.com>
 <AM0PR03MB60820BB9108F66ACB2892F6697100@AM0PR03MB6082.eurprd03.prod.outlook.com>
Message-ID: <D5B5EB2E-DCAE-4706-B2A2-6936EE46D99D@donders.ru.nl>

Hi Kris,

I think that Eelke meant that the Z-scoring leads to the threshold becoming independent of the signals’ physical units.
I agree that the signals have a non-Gaussian distribution, but this is equally true for non-envelope signals.
Personally I think that normalisation with an estimate of the median or mad at this stage of an analysis pipeline is not going to change the outcome of the science much (i.e. the inferential decisions), but if you have a good implementation of this, we could certainly build this in as an option. I would however welcome much more improvements to the way that we compute our test-statistics that we use for inferential decision making, e.g. using Yuen-Welch T-statistics based on trimmed means and variances, rather than the good old T-statistic.

Feel free to submit your version of the code as a PR to the github repository.


Best wishes,

Jan-Mathijs

On 19 Feb 2020, at 13:13, De Meyer, Kris <kris.de_meyer at kcl.ac.uk<mailto:kris.de_meyer at kcl.ac.uk>> wrote:

Thank you for your response, Eelke.

I guess it makes sense but it does make the selection of a threshold more arbitrary.

If your underlying distribution is normal, then a z-score of 3, 4 or 5 has a clear meaning in terms of outlier detection.

For a non-Gaussian distribution, that interpretation no longer holds, and rejection becomes less automated and more open to subjective interpretation.

Isn't it better to z-transform the Hilbert-envelope values with the mean/std or the median/mad of the original filtered EEG distribution rather than the mean/std or median/mad of the hilbert values distribution? That way, the meaning of the threshold magnitude would remain valid. Or is that what is happening in the code already?

Best,

Kris



________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Eelke Spaak <e.spaak at donders.ru.nl<mailto:e.spaak at donders.ru.nl>>
Sent: 18 February 2020 10:45
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] question about automatic artefact rejection

Dear Kris,

Since there is no statistical test involved, I see no problems with
computing a z-score here. Think of it more as bringing the data into a
sensible range and allowing yourself to forget about details like
measurement unit etc. You could also not do the z-transform, and
simply specify a threshold based on raw amplitude, this would be
equivalent (but might make it potentially more difficult to come up
with a good threshold).

Best,
Eelke

On Tue, 18 Feb 2020 at 09:47, De Meyer, Kris <kris.de_meyer at kcl.ac.uk<mailto:kris.de_meyer at kcl.ac.uk>> wrote:
>
> Dear Fieldtrippers,
>
> In ft_artifact_muscle, an EEG signal is first filtered - usually with a bandpass filter with cutoff frequencies of [110,140]. The documentation then says that the hilbert envelope is calculated, after which the envelope values are z-transformed before they are thresholded.
>
> However, is this sound? Whereas the actual filtered EEG values (the result of the bandpass filter) are usually normally distributed, the hilbert envelope values are far from.
>
> What is the rationale for calculating the z-transform of a non-Gaussian distribution? Doesn't that introduce problems?
>
> Best,
>
> Kris
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=miiXPIhNF0zd23xrFrXakUxAUldGY6DZLnhoajNtLlg%3D&amp;reserved=0
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0

_______________________________________________
fieldtrip mailing list
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https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0
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https://doi.org/10.1371/journal.pcbi.1002202

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From anya_ml at wp.pl  Wed Feb 19 14:06:24 2020
From: anya_ml at wp.pl (Anna Grochowska)
Date: Wed, 19 Feb 2020 14:06:24 +0100
Subject: [FieldTrip] question about automatic artefact rejection
In-Reply-To: <D5B5EB2E-DCAE-4706-B2A2-6936EE46D99D@donders.ru.nl>
References: <AM0PR03MB60820E9A9469986E0E7DD87497160@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <AM0PR03MB6082896FB472BD7759940BA497110@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <CABPNLUp-+Baq4zTruv5bhH76B6tpQ3Tudk-4jJ-VBBnDW6Hcfg@mail.gmail.com>
 <AM0PR03MB60820BB9108F66ACB2892F6697100@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <D5B5EB2E-DCAE-4706-B2A2-6936EE46D99D@donders.ru.nl>
Message-ID: <074BBABC-F088-4B5B-A6CC-4CE2B88ED8B3@wp.pl>

Please, don’t add my email to your conversation.
AG


> Wiadomość napisana przez Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl> w dniu 19.02.2020, o godz. 13:25:
> 
> Hi Kris,
> 
> I think that Eelke meant that the Z-scoring leads to the threshold becoming independent of the signals’ physical units.
> I agree that the signals have a non-Gaussian distribution, but this is equally true for non-envelope signals.
> Personally I think that normalisation with an estimate of the median or mad at this stage of an analysis pipeline is not going to change the outcome of the science much (i.e. the inferential decisions), but if you have a good implementation of this, we could certainly build this in as an option. I would however welcome much more improvements to the way that we compute our test-statistics that we use for inferential decision making, e.g. using Yuen-Welch T-statistics based on trimmed means and variances, rather than the good old T-statistic.
> 
> Feel free to submit your version of the code as a PR to the github repository.
> 
> 
> Best wishes,
> 
> Jan-Mathijs
> 
>> On 19 Feb 2020, at 13:13, De Meyer, Kris <kris.de_meyer at kcl.ac.uk <mailto:kris.de_meyer at kcl.ac.uk>> wrote:
>> 
>> Thank you for your response, Eelke.
>> 
>> I guess it makes sense but it does make the selection of a threshold more arbitrary. 
>> 
>> If your underlying distribution is normal, then a z-score of 3, 4 or 5 has a clear meaning in terms of outlier detection. 
>> 
>> For a non-Gaussian distribution, that interpretation no longer holds, and rejection becomes less automated and more open to subjective interpretation.
>> 
>> Isn't it better to z-transform the Hilbert-envelope values with the mean/std or the median/mad of the original filtered EEG distribution rather than the mean/std or median/mad of the hilbert values distribution? That way, the meaning of the threshold magnitude would remain valid. Or is that what is happening in the code already?
>> 
>> Best,
>> 
>> Kris
>> 
>> 
>> 
>> From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Eelke Spaak <e.spaak at donders.ru.nl <mailto:e.spaak at donders.ru.nl>>
>> Sent: 18 February 2020 10:45
>> To: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>>
>> Subject: Re: [FieldTrip] question about automatic artefact rejection
>>  
>> Dear Kris,
>> 
>> Since there is no statistical test involved, I see no problems with
>> computing a z-score here. Think of it more as bringing the data into a
>> sensible range and allowing yourself to forget about details like
>> measurement unit etc. You could also not do the z-transform, and
>> simply specify a threshold based on raw amplitude, this would be
>> equivalent (but might make it potentially more difficult to come up
>> with a good threshold).
>> 
>> Best,
>> Eelke
>> 
>> On Tue, 18 Feb 2020 at 09:47, De Meyer, Kris <kris.de_meyer at kcl.ac.uk <mailto:kris.de_meyer at kcl.ac.uk>> wrote:
>> >
>> > Dear Fieldtrippers,
>> >
>> > In ft_artifact_muscle, an EEG signal is first filtered - usually with a bandpass filter with cutoff frequencies of [110,140]. The documentation then says that the hilbert envelope is calculated, after which the envelope values are z-transformed before they are thresholded.
>> >
>> > However, is this sound? Whereas the actual filtered EEG values (the result of the bandpass filter) are usually normally distributed, the hilbert envelope values are far from.
>> >
>> > What is the rationale for calculating the z-transform of a non-Gaussian distribution? Doesn't that introduce problems?
>> >
>> > Best,
>> >
>> > Kris
>> >
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > fieldtrip mailing list
>> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=miiXPIhNF0zd23xrFrXakUxAUldGY6DZLnhoajNtLlg%3D&amp;reserved=0 <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=miiXPIhNF0zd23xrFrXakUxAUldGY6DZLnhoajNtLlg%3D&amp;reserved=0>
>> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0 <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0>
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=miiXPIhNF0zd23xrFrXakUxAUldGY6DZLnhoajNtLlg%3D&amp;reserved=0 <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=miiXPIhNF0zd23xrFrXakUxAUldGY6DZLnhoajNtLlg%3D&amp;reserved=0>
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0 <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&amp;data=01%7C01%7Ckris.de_meyer%40kcl.ac.uk%7C87c72918f62a46527c2408d7b4676f15%7C8370cf1416f34c16b83c724071654356%7C0&amp;sdata=DNmcynQGcA4%2FAmDi8PSk8UE%2FBfy0Ce8yGRPr3Cv%2BvZ8%3D&amp;reserved=0>
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip <https://mailman.science.ru.nl/mailman/listinfo/fieldtrip>
>> https://doi.org/10.1371/journal.pcbi.1002202 <https://doi.org/10.1371/journal.pcbi.1002202>
> 
> _______________________________________________
> fieldtrip mailing list
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> https://doi.org/10.1371/journal.pcbi.1002202

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From kris.de_meyer at kcl.ac.uk  Wed Feb 19 14:12:14 2020
From: kris.de_meyer at kcl.ac.uk (De Meyer, Kris)
Date: Wed, 19 Feb 2020 13:12:14 +0000
Subject: [FieldTrip] question about automatic artefact rejection
In-Reply-To: <D5B5EB2E-DCAE-4706-B2A2-6936EE46D99D@donders.ru.nl>
References: <AM0PR03MB60820E9A9469986E0E7DD87497160@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <AM0PR03MB6082896FB472BD7759940BA497110@AM0PR03MB6082.eurprd03.prod.outlook.com>
 <CABPNLUp-+Baq4zTruv5bhH76B6tpQ3Tudk-4jJ-VBBnDW6Hcfg@mail.gmail.com>
 <AM0PR03MB60820BB9108F66ACB2892F6697100@AM0PR03MB6082.eurprd03.prod.outlook.com>,
 <D5B5EB2E-DCAE-4706-B2A2-6936EE46D99D@donders.ru.nl>
Message-ID: <AM0PR03MB6082FE51910324009E53060697100@AM0PR03MB6082.eurprd03.prod.outlook.com>

Thanks for the clarification, Jan Mathijs.

In the data I've looked at, the histogram of a [110,140]Hz bandpass-filtered signal usually is pretty Gaussian if not affected by EMG noise, but becomes more an more heavy-tailed the more EMG noise is present.

I didn't yet mention that in my research, I look at high-gamma frequencies (anything up to 170Hz) so I have a feeling that there might be an impact on inferential statistics if data contaminated with EMG is not adequately excluded.

I'll test this approach further to see what happens.

Best,

Kris


________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl>
Sent: 19 February 2020 12:25
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] question about automatic artefact rejection

Hi Kris,

I think that Eelke meant that the Z-scoring leads to the threshold becoming independent of the signals’ physical units.
I agree that the signals have a non-Gaussian distribution, but this is equally true for non-envelope signals.
Personally I think that normalisation with an estimate of the median or mad at this stage of an analysis pipeline is not going to change the outcome of the science much (i.e. the inferential decisions), but if you have a good implementation of this, we could certainly build this in as an option. I would however welcome much more improvements to the way that we compute our test-statistics that we use for inferential decision making, e.g. using Yuen-Welch T-statistics based on trimmed means and variances, rather than the good old T-statistic.

Feel free to submit your version of the code as a PR to the github repository.


Best wishes,

Jan-Mathijs

On 19 Feb 2020, at 13:13, De Meyer, Kris <kris.de_meyer at kcl.ac.uk<mailto:kris.de_meyer at kcl.ac.uk>> wrote:

Thank you for your response, Eelke.

I guess it makes sense but it does make the selection of a threshold more arbitrary.

If your underlying distribution is normal, then a z-score of 3, 4 or 5 has a clear meaning in terms of outlier detection.

For a non-Gaussian distribution, that interpretation no longer holds, and rejection becomes less automated and more open to subjective interpretation.

Isn't it better to z-transform the Hilbert-envelope values with the mean/std or the median/mad of the original filtered EEG distribution rather than the mean/std or median/mad of the hilbert values distribution? That way, the meaning of the threshold magnitude would remain valid. Or is that what is happening in the code already?

Best,

Kris



________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Eelke Spaak <e.spaak at donders.ru.nl<mailto:e.spaak at donders.ru.nl>>
Sent: 18 February 2020 10:45
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] question about automatic artefact rejection

Dear Kris,

Since there is no statistical test involved, I see no problems with
computing a z-score here. Think of it more as bringing the data into a
sensible range and allowing yourself to forget about details like
measurement unit etc. You could also not do the z-transform, and
simply specify a threshold based on raw amplitude, this would be
equivalent (but might make it potentially more difficult to come up
with a good threshold).

Best,
Eelke

On Tue, 18 Feb 2020 at 09:47, De Meyer, Kris <kris.de_meyer at kcl.ac.uk<mailto:kris.de_meyer at kcl.ac.uk>> wrote:
>
> Dear Fieldtrippers,
>
> In ft_artifact_muscle, an EEG signal is first filtered - usually with a bandpass filter with cutoff frequencies of [110,140]. The documentation then says that the hilbert envelope is calculated, after which the envelope values are z-transformed before they are thresholded.
>
> However, is this sound? Whereas the actual filtered EEG values (the result of the bandpass filter) are usually normally distributed, the hilbert envelope values are far from.
>
> What is the rationale for calculating the z-transform of a non-Gaussian distribution? Doesn't that introduce problems?
>
> Best,
>
> Kris
>
>
>
>
>
> _______________________________________________
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From Joachim.Lange at med.uni-duesseldorf.de  Wed Feb 19 15:15:56 2020
From: Joachim.Lange at med.uni-duesseldorf.de (Joachim.Lange at med.uni-duesseldorf.de)
Date: Wed, 19 Feb 2020 14:15:56 +0000
Subject: [FieldTrip] positions of Neuromag sensors rotated
Message-ID: <e9d298c450a441cb8fc51c054f268a8c@med.uni-duesseldorf.de>

Dear Fieldtrippers,
I'm not sure whether my problem is a Fieldtrip or a Neuromag problem, but maybe someone can help me here.

I've recorded MEG data with a Neuromag system and the headshape and hpi coils using the polhemus system. When I read the headshape and the sensor locations from the fif-file and plot them using Fieldtrip, the plots look as expected, i.e., the "headshape" and the hpi coils are located within the MEG sensors / helmet (see attached example figures S1_1 and S1_2 from different angles). For one subject, however, the sensors from the hdr.grad-file seem rotated and it even looks like the "headshape" is partly outside the MEG sensors / helmet (see attached figures S2_1 and S2_2).
I have no idea what is going wrong here and/or how I could correct the apparently wrong positions. Any help would be much appreciated.
Thanks,
Jo

Ps: the simple FT-code:

hdr = ft_read_header('subject.fif');
headshape = ft_read_headshape('subject.fif');
figure;
ft_plot_sens(hdr.grad, 'style', 'b.', 'coil', 'false');
ft_plot_mesh(headshape.pos(1:4,:),'vertexsize',20,'vertexcolor','r'); %HPI coils
ft_plot_mesh(headshape.pos(5:end,:),'vertexsize',20,'vertexcolor','k'); %"manual" headshape
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From anya_ml at wp.pl  Wed Feb 19 15:59:47 2020
From: anya_ml at wp.pl (Anna Grochowska)
Date: Wed, 19 Feb 2020 15:59:47 +0100
Subject: [FieldTrip] Chile EEG workshop
In-Reply-To: <glx1y0-an8bwbwa6tv3-5oln99-u0i50qvquwcuna3aki-lzdjxv-fe7zf7-vs6cr-d42u4edbuatu69hje2f9p85v-t6rhktr6b0bhekso7l-srgnzn-5szivkfry748ere5eh-w5rreyzdb0sf121dex.1581951598265@email.android.com>
References: <glx1y0-an8bwbwa6tv3-5oln99-u0i50qvquwcuna3aki-lzdjxv-fe7zf7-vs6cr-d42u4edbuatu69hje2f9p85v-t6rhktr6b0bhekso7l-srgnzn-5szivkfry748ere5eh-w5rreyzdb0sf121dex.1581951598265@email.android.com>
Message-ID: <1CF6DF2A-CE19-48F8-A6AC-23A0A90DCFAE@wp.pl>

Hello, 
Could you unsubscribe my email?
Thank you
Anna Grochowska

> Wiadomość napisana przez anya_ml at wp.pl w dniu 17.02.2020, o godz. 15:59:
> 
> 
> Hello,
> Could you precise if the Chile EEG workshop will take place during summer (July-September) or it will be other date? And what is the subject, eeg analysis in fieldtrip toolbox or rather clinical eeg preparation? 
> Thank you for the answer
> Anna Grochowska
> University of Warsaw
> 

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From martin.rosenfelder at uni-ulm.de  Wed Feb 19 16:16:47 2020
From: martin.rosenfelder at uni-ulm.de (Martin Rosenfelder)
Date: Wed, 19 Feb 2020 16:16:47 +0100
Subject: [FieldTrip] Chile EEG workshop
In-Reply-To: <1CF6DF2A-CE19-48F8-A6AC-23A0A90DCFAE@wp.pl>
References: <glx1y0-an8bwbwa6tv3-5oln99-u0i50qvquwcuna3aki-lzdjxv-fe7zf7-vs6cr-d42u4edbuatu69hje2f9p85v-t6rhktr6b0bhekso7l-srgnzn-5szivkfry748ere5eh-w5rreyzdb0sf121dex.1581951598265@email.android.com>
 <1CF6DF2A-CE19-48F8-A6AC-23A0A90DCFAE@wp.pl>
Message-ID: <091a62dd-85cd-f978-e3e0-a5ba7b652984@uni-ulm.de>

Dear Anna,

You can unsubscribe from the mailing list using this link
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Just follow the instructions on the bottom of the page to unsubscribe.

Best,
Martin

Am 19.02.20 um 15:59 schrieb Anna Grochowska:
> Hello,
> Could you unsubscribe my email?
> Thank you
> Anna Grochowska
>
>> Wiadomość napisana przez anya_ml at wp.pl <mailto:anya_ml at wp.pl> w dniu 
>> 17.02.2020, o godz. 15:59:
>>
>>
>> Hello,
>> Could you precise if the Chile EEG workshop will take place during 
>> summer (July-September) or it will be other date? And what is the 
>> subject, eeg analysis in fieldtrip toolbox or rather clinical eeg 
>> preparation?
>> Thank you for the answer
>> Anna Grochowska
>> University of Warsaw
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202

-- 
M.Sc.-Psych. Martin Rosenfelder
Research Associate
PhD Student
Clinical and Biological Psychology
Ulm University
Room: 47.2.259
Phone: +49 731-50 26592
E-mail: martin.rosenfelder at uni-ulm.de

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From alexandra.korzeczek at med.uni-goettingen.de  Wed Feb 19 18:14:08 2020
From: alexandra.korzeczek at med.uni-goettingen.de (Korzeczek, Alexandra)
Date: Wed, 19 Feb 2020 17:14:08 +0000
Subject: [FieldTrip] Sourcegrandaverage error due to different "inside"
 values
Message-ID: <C8AC65C5CF8A3B46B5A6AB5B365E944491C2BA22@umg-exc-3.ads.local.med.uni-goettingen.de>

Dear Fieldtrip community,

has anyone a suggestion what might be my mistake for not being able to run ft_sourcegrandaverage over several subjects?
I am using FT version (20180906) applying beamformer on each individual subject prior to normalize individual subjects to MNI space.
I receive the error message: Error using ft_sourcegrandaverage (line 116), the input sources vary in the field.
This error is due to different values of my "src.inside" field. Some years ago (https://mailman.science.ru.nl/pipermail/fieldtrip/2015-October/009709.html)
the same error was solved by adding the pos of a template. However, this does not work with my data.
Am I using a wrong template maybe? My original dimensions after using sourceinterpolate are [160,160,128].

The datainput to sourcegrandaverage (and output of ft_volumenormalise) looks like that:
src_mni.anatomy   [181x217x181] double
src_mni.pow           [181x217x181] double
src_mni.inside        [181x217x181] logical
src_mni.transform 4x4 double
src_mni.dim           [181,217,181]
src_mni.params     1x1 struct
src_mni.initial        4x4 double
src_mni.coordsys  'spm'
src_mni.cfg            1x1 struct

My script is:
% source interpolate
cfg  = [];
cfg.parameter = 'pow';
src_interp  = ft_sourceinterpolate(cfg, src , realmri);

% normalize to MNI
cfg  = [];
cfg.nonlinear = 'no';
src_mni  = ft_volumennormalise(cfg, src_interp);


Thanks,
Alexandra


_____________________________________
Alexandra Korzeczek
PhD Student | BeCog Geog-August-Universität Göttingen
University Medicine Göttingen | Dept. of Clinical Neurophysiology




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From anya_ml at wp.pl  Wed Feb 19 20:46:36 2020
From: anya_ml at wp.pl (Anna Grochowska)
Date: Wed, 19 Feb 2020 20:46:36 +0100
Subject: [FieldTrip] Chile EEG workshop
In-Reply-To: <glx1y0-an8bwbwa6tv3-5oln99-u0i50qvquwcuna3aki-lzdjxv-fe7zf7-vs6cr-d42u4edbuatu69hje2f9p85v-t6rhktr6b0bhekso7l-srgnzn-5szivkfry748ere5eh-w5rreyzdb0sf121dex.1581951598265@email.android.com>
References: <glx1y0-an8bwbwa6tv3-5oln99-u0i50qvquwcuna3aki-lzdjxv-fe7zf7-vs6cr-d42u4edbuatu69hje2f9p85v-t6rhktr6b0bhekso7l-srgnzn-5szivkfry748ere5eh-w5rreyzdb0sf121dex.1581951598265@email.android.com>
Message-ID: <3DF5429B-2358-4C7C-86AD-8F38073324E6@wp.pl>

Could you answer my question from above about Chile EEG workshop?
Thank you
AG

> Wiadomość napisana przez anya_ml at wp.pl w dniu 17.02.2020, o godz. 15:59:
> 
> 
> Hello,
> Could you precise if the Chile EEG workshop will take place during summer (July-September) or it will be other date? And what is the subject, eeg analysis in fieldtrip toolbox or rather clinical eeg preparation? 
> Thank you for the answer
> Anna Grochowska
> University of Warsaw
> 

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From ffein at stanford.edu  Wed Feb 19 21:08:47 2020
From: ffein at stanford.edu (Franklin Feingold)
Date: Wed, 19 Feb 2020 20:08:47 +0000
Subject: [FieldTrip] BIDS 1.2.2 release and Genetic Information feedback
Message-ID: <431036E3-ADE5-4E0A-979A-B8769404A0CC@stanford.edu>

We are excited to announce the release of BIDS version 1.2.2! This release enhanced the specification through additional clarifications and smaller fixes. The new recently released versions can be found at: https://bids-specification.readthedocs.io/en/stable/ along with the complete changelog<https://bids-specification.readthedocs.io/en/stable/CHANGES.html>.



In addition, BIDS is calling a final round of comments on the Genetic Information<https://github.com/bids-standard/bids-specification/pull/395>

extension proposal<https://github.com/bids-standard/bids-specification/pull/395>! Please review this extension proposal and leave your feedback - we aim to merge this extension soon!



Shout out to the Genetic Information BIDS Extension Proposal leads: Cyril Pernet, Clara Moreau, Tom

Nichols, and Jessica Turner!



Thank you!


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From alu0101305493 at ull.edu.es  Thu Feb 20 18:24:47 2020
From: alu0101305493 at ull.edu.es (ANQI ZANG)
Date: Thu, 20 Feb 2020 17:24:47 +0000
Subject: [FieldTrip] About waveguard 64 channel layout
Message-ID: <CAKyW_3TPbrtPFKjYVv9tBoTs42+ebi90pofeRaRqCqY58hLyUA@mail.gmail.com>

Dear all,
I am using fieldtrip to preprocess my data recently.
I am using ANT Neuro wave guard original 64-channel EEG cap for my study
and I can't find the lelectrod layout file online. It is also difficult to
find 2D template position for me. I try to use an image to make the layout
myself, but the location is not very precise. Is there any other way to
work this out?
Thank you very much.
Anqi
PhD Candidate
Instituto Universitario de Neurociencia
Universidad de La Laguna
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From alexandra.korzeczek at med.uni-goettingen.de  Thu Feb 20 18:48:46 2020
From: alexandra.korzeczek at med.uni-goettingen.de (Korzeczek, Alexandra)
Date: Thu, 20 Feb 2020 17:48:46 +0000
Subject: [FieldTrip] scalp is plotted in template sourcemodel & AW:
 Sourcegrandaverage error due to different "inside" values
Message-ID: <C8AC65C5CF8A3B46B5A6AB5B365E944491C303E3@umg-exc-3.ads.local.med.uni-goettingen.de>

Dear all,

just to answer my own question: my mistake was not to apply a template grid on individual subjects.
See tutorial step: Performing group analysis on 3-dimensional source-reconstructed data<http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#performing-group-analysis-on-3-dimensional-source-reconstructed-data>.

However, I have a follow-up question:
When I plot the sourcemodel/grid (calculated by a template and the individual mri) not the brain as shown in the tutorial but the scalp is plotted. The "scalp -sourcemodel" plot remains, even when using the example mri. Should I use the segmented mri as input to ft_prepare_sourcemodel instead?

FROM FIELDTRIP tutorial:
%% compute the source model
cfg = [];
cfg.warpmni   = 'yes';
cfg.template  = template.sourcemodel;
cfg.nonlinear = 'yes'; % use non-linear normalization
cfg.mri            = mri; ## HERE Use segementedmri?

sourcemodel        = ft_prepare_sourcemodel(cfg);


Thanks and Best,
Alexandra


Von: fieldtrip <fieldtrip-bounces at science.ru.nl> Im Auftrag von Korzeczek, Alexandra
Gesendet: Mittwoch, 19. Februar 2020 18:14
An: FieldTrip discussion list <fieldtrip at science.ru.nl>
Betreff: [FieldTrip] Sourcegrandaverage error due to different "inside" values

Dear Fieldtrip community,

has anyone a suggestion what might be my mistake for not being able to run ft_sourcegrandaverage over several subjects?
I am using FT version (20180906) applying beamformer on each individual subject prior to normalize individual subjects to MNI space.
I receive the error message: Error using ft_sourcegrandaverage (line 116), the input sources vary in the field.
This error is due to different values of my "src.inside" field. Some years ago (https://mailman.science.ru.nl/pipermail/fieldtrip/2015-October/009709.html)
the same error was solved by adding the pos of a template. However, this does not work with my data.
Am I using a wrong template maybe? My original dimensions after using sourceinterpolate are [160,160,128].

The datainput to sourcegrandaverage (and output of ft_volumenormalise) looks like that:
src_mni.anatomy   [181x217x181] double
src_mni.pow           [181x217x181] double
src_mni.inside        [181x217x181] logical
src_mni.transform 4x4 double
src_mni.dim           [181,217,181]
src_mni.params     1x1 struct
src_mni.initial        4x4 double
src_mni.coordsys  'spm'
src_mni.cfg            1x1 struct

My script is:
% source interpolate
cfg  = [];
cfg.parameter = 'pow';
src_interp  = ft_sourceinterpolate(cfg, src , realmri);

% normalize to MNI
cfg  = [];
cfg.nonlinear = 'no';
src_mni  = ft_volumennormalise(cfg, src_interp);


Thanks,
Alexandra


_____________________________________
Alexandra Korzeczek
PhD Student | BeCog Geog-August-Universität Göttingen
University Medicine Göttingen | Dept. of Clinical Neurophysiology




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From cristinarainich at gmail.com  Thu Feb 20 23:13:22 2020
From: cristinarainich at gmail.com (Kristina Rainich)
Date: Fri, 21 Feb 2020 01:13:22 +0300
Subject: [FieldTrip] MEG NORD 2020 conference
Message-ID: <CA+pjZuUR2tSuFiUmkrZJSV2WqDjE7rh=i+o+5XmRLWFDsPN0JQ@mail.gmail.com>

Dear all,

We are excited to announce the preliminary agenda for the MEG NORD 2020 (
https://megnord.org/) happening in Moscow, Russia May 25-27th, 2020.

The first day there will be a workshop on data analysis in MNE-Python held
by Alex Gramfort and the keynote lectures by Vadim Nikulin and Yoshio
Okada. The second and third days we will host the keynote lectures by Matt
Brookes and Nathan Weisz, site presentations from North European leading
contributors in the MEG field, blitz talks and poster presentations!
There is *no* cost for registration but please do send us an email if you
plan to attend. The agenda and registration can be found at the website:
https://megnord.org/.

The deadline for registration and abstract submission for poster
presentation is *1st March 2020.*
To register please forward an email with your name, affiliation to
2020 at megnord.org and also state whether you would like to participate in
the workshop (please out the subject of the email as follows:
REGISTRATION). If you want to present a poster, please add a *title,
authors list, affiliations and abstract* (250 words max) to the letter
about registration (the subject of the email: ABSTRACT SUBMISSION).

Please note that the information on venues, lodging, poster presentation,
and a detailed schedule of the conference will be available on the MEG NORD
website in March.

We will issue an invitation letter for your VISA to Russia, and support you
with all the necessary information.

We would really appreciate if you can spread the word about the conference
to research groups, students, postdocs, etc. that you may know.

See you in Moscow!

Best Regards,
MEG NORD 2020 Organization Committee
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From mireia.torralba at upf.edu  Mon Feb 24 18:17:26 2020
From: mireia.torralba at upf.edu (TORRALBA CUELLO, MIREIA)
Date: Mon, 24 Feb 2020 18:17:26 +0100
Subject: [FieldTrip] Possible bug in mtmconvol padding option
Message-ID: <CALWZVf6kiji5FXt16MKKrL+T5SaYkH0N4mFRC4Tf-X8xTeU0Uw@mail.gmail.com>

Hi,
I am a Fieldtrip user and I came across this error

ft_error('the specified padding is too short');

when calculating power spectrum using this code:

 cfg=[];
    cfg.method='mtmconvol';
    cfg.foi=2:1:40;
    cfg.t_ftimwin=0.5*ones(length(cfg.foi),1);
    cfg.pad=1;
cfg.taper='hanning';
fLast=ft_freqanalysis(cfg,dataLast);

As I see it, the padding should work in each of my time windows (0.5
seconds length each) and therefore the error should not appear, but when I
inspected which is the segment padded by the function I saw
that what is being padded to 1 is the whole segment. I think this is not
right, as what I would like is to increase my frequency resolution by
padding each of the timewindows where I calculate the spectrum. The problem
I have is that I want to use as a baseline another segment which has 0.5
seconds length, and as the frequency extracted by mtmconvol depends on the
length of the segment, I am getting different frequency resolutions for the
baseline and the target data.

Can anyone help me?
Thanks and best regards.

Mireia



Mireia Torralba Cuello
Multisensory Research Group
Center for Brain and Cognition, Universitat Pompeu Fabra
Address: Edifici Mercè Rodoreda 24.313
        c\ Ramon Trias Fargas, 25-27
        08005 Barcelona
http://www.mrg.upf.edu
Tel +34 935422745
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From z65.juhasz at gmail.com  Tue Feb 25 13:46:49 2020
From: z65.juhasz at gmail.com (Zoltan Juhasz)
Date: Tue, 25 Feb 2020 13:46:49 +0100
Subject: [FieldTrip] Problem with Beamformer demo
Message-ID: <CANxafJ=attViuffT+a22T4AB_2_MOCb5kQC1gpyGZu6CLFFExQ@mail.gmail.com>

 I have recently run into a problem while executing the Beamformer
Fieldtrip demo at http://www.fieldtriptoolbox.org/tutorial/beamformer/

I am using the sample data set and the source code from this page but the
picture I get for the section "Source Analysis: Contrast activity to
another interval" is rather strange. I include here the 3 outputs, first
two are correct, third one is the problematic one. Also included is the
source. Matlab version used: R2019a. Could someone check whether it is a
script error or perhaps a change in Matlab that generates the odd result?

links to figures and source:
https://drive.google.com/drive/folders/1XPZd5l3og1WAEt8dK6Bx7a9W8xgSzCMF?usp=sharing

Thanks,
Zoltan
University of Pannonia, Hungary
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From huiyu_kang at fudan.edu.cn  Wed Feb 26 09:17:51 2020
From: huiyu_kang at fudan.edu.cn (=?UTF-8?B?5bq35oWn5a6H?=)
Date: Wed, 26 Feb 2020 16:17:51 +0800 (GMT+08:00)
Subject: [FieldTrip] Post-doc Positions | Neural and Intelligence
 Engineering Center,
 Institute of Science and Technology for Brain-inspired Intelligence
Message-ID: <25a2b8a8.919c.1708092d691.Coremail.huiyu_kang@fudan.edu.cn>

The positions are supported by Shanghai Government Key Project of ‘Brain and Brain-inspired Intelligence’($125 Millions), and are affiliated with the Neural and Intelligence Engineering Center led by Prof. Shouyan Wang, Vice-dean of Institute of Science and Technology for Brain-Inspired Intelligence (ISTBI), Fudan University. The projects will collaborate with Professor Peter Brown (https://www.ndcn.ox.ac.uk/team/peter-brown) and Professor Timothy Denison (http://www.ibme.ox.ac.uk/research/bioelectronic-medicine/tim-denison) at University of Oxford, and Professors Trevor Robbins (https://www.neuroscience.cam.ac.uk/directory/profile.php?Trevor) and Barbara Sahakian (https://www.neuroscience.cam.ac.uk/directory/profile.php?barbara) at University of Cambridge.

Research Projects:

l  Neural decoding in neuropathic pain, movement disorders and depression

l  Intelligent neuromodulation of deep brain stimulation andtranscranial electrical stimulation in neuropathic pain, movement disorders and depression

l  Big data analysis and electronic health (e-Health) for brain disorders

l  Consciousness and cognition intervention in depression

Qualifications:

(1) Researchers who will receive PhD soon or graduated within last five years.

(2) Under 35 years old.Excellent candidates aged 35 to 38 may be considered.

(3) Research experience in machine learning, neural signal processing,  biomedical electronics or neurophysiology in pain, movement disorders or depression, or related research experience in neuroscience or psychology.

Benefits：

1.     The initial employment period is 2 years and extendable up to 4 years according to project progress.

2.     Salary is ¥300k ~400k /year ($43k~58k / year).

3.     Additional research funding up to $30k provided to support researchers with excellent ideas and independent capability.

4.     Opportunities to top-up salaries up to $14k / year with grant from Shanghai Government.

5.     Opportunities to have research visiting at University of Oxford, University of Cambridge or Harvard University.

6.     Opportunities to transfer to faculty position with start-up of $72k~144k.

7.     In accordance with the policies of Fudan University, assist children of the candidates to apply for admission to kindergartens or primary school affiliated to Fudan University.

Application Procedure：

Send CV with contact information of referees, cover letter and PDF of key publications to shouyan at fudan.edu.cn and niec_istbi at fudan.edu.cn with e-mail subject Post-doc Application+Connectionists.

Additional Information

Fudan University is one of the top five universities in China, and ranked at #105 in Times Higher Education World University Ranking. ISTBI is a leading institute in brain-inspired artificial intelligence, neuroimaging, biomedical big data and neural engineering in China. More information can be found from https://www.fudan.edu.cn/en/ and https://istbi.fudan.edu.cn/lnen/. 




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From azizi.sima.67 at gmail.com  Thu Feb 27 01:36:28 2020
From: azizi.sima.67 at gmail.com (sima azizi)
Date: Wed, 26 Feb 2020 18:36:28 -0600
Subject: [FieldTrip] original standard 10-20 channel Positions
Message-ID: <CAKEoKp8kR2pR=7CDtiuk+Eq6sb8Yto9VMhE2BwLW2xPoZ6j7xQ@mail.gmail.com>

Dear Fieldtrip members,

I am a PhD candidate at MST in Electrical engineering.I have recently been
using fieldtrip to do the source reconstruction.

The EEG data set that I am working with, is recorded using the original
standard 10-20  montage with 19 channels. In terms of finding the channel
positions for the forward problem, I use the template "standard_1020.elec"
which has the 97 channels.

I know my question is trivial, but instead of extended version of standard
10-20 montage, I need original one which has the 19 channels. Is there a
template for the original one or do I need to remove the extra channels? If
I need to remove the channels, how should I do that?


Best regards,
Sima.
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From azizi.sima.67 at gmail.com  Thu Feb 27 02:25:17 2020
From: azizi.sima.67 at gmail.com (sima azizi)
Date: Wed, 26 Feb 2020 19:25:17 -0600
Subject: [FieldTrip] original standard 10-20 channel Positions
In-Reply-To: <CAKEoKp8kR2pR=7CDtiuk+Eq6sb8Yto9VMhE2BwLW2xPoZ6j7xQ@mail.gmail.com>
References: <CAKEoKp8kR2pR=7CDtiuk+Eq6sb8Yto9VMhE2BwLW2xPoZ6j7xQ@mail.gmail.com>
Message-ID: <CAKEoKp-8=KzyYFkVk9k72stYO2KNH160+_79=b22ooH2pOpzgw@mail.gmail.com>

Dear all,

The labels of the EEG data set that I am working with is different from the
labels in the "standard_1020.elec" template. (both the labels and
the number of channels and electrodes)
Does anybody know how should I specify the EEG positions to solve the
forward problem?

Data were acquired with the sampling frequency of 250 Hz using the standard
1020 EEG montage with 19 EEG channels: Fp1, Fp2, F7, F3, Fz, F4, F8, T3,
C3, Cz, C4, T4, T5,
P3, Pz, P4, T6, O1, O2. The reference electrode was placed at FCz.

I appreciate any help in this regard.
Best regards,
Sima.

On Wed, Feb 26, 2020 at 6:36 PM sima azizi <azizi.sima.67 at gmail.com> wrote:

> Dear Fieldtrip members,
>
> I am a PhD candidate at MST in Electrical engineering.I have recently been
> using fieldtrip to do the source reconstruction.
>
> The EEG data set that I am working with, is recorded using the original
> standard 10-20  montage with 19 channels. In terms of finding the channel
> positions for the forward problem, I use the template "standard_1020.elec"
> which has the 97 channels.
>
> I know my question is trivial, but instead of extended version of standard
> 10-20 montage, I need original one which has the 19 channels. Is there a
> template for the original one or do I need to remove the extra channels? If
> I need to remove the channels, how should I do that?
>
>
> Best regards,
> Sima.
>
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From jan.schoffelen at donders.ru.nl  Thu Feb 27 09:29:15 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 27 Feb 2020 08:29:15 +0000
Subject: [FieldTrip] Possible bug in mtmconvol padding option
In-Reply-To: <CALWZVf6kiji5FXt16MKKrL+T5SaYkH0N4mFRC4Tf-X8xTeU0Uw@mail.gmail.com>
References: <CALWZVf6kiji5FXt16MKKrL+T5SaYkH0N4mFRC4Tf-X8xTeU0Uw@mail.gmail.com>
Message-ID: <65ACF498-3854-4EBD-AAA9-9BDFF4763AFD@donders.ru.nl>

Hi Mireia,

Indeed the cfg.pad parameter operates on the full epoch length, not on the sliding window length. This is per design, and it is not a bug.

Although I don’t fully understand the deeper reason of why you want to do what you want to do, one way to get there would be to handcraft your own procedure, and create the TFRs in a computationally inefficient for-loop. This would require a lot of data bookkeeping on your end.

Procedurally:

for k = 1:the-number-of-time-point-onto-which-you-want-to-estimate-your-tfr

  cfg = [];
  cfg.latency = timepoint(k)+[-0.25 0.25-1./data.fsample];
  tmpdata = ft_selectdata(cfg, data);

  cfg = [];
  cfg.pad = 0.5;
  cfg.method = ‘mtmfft’;
  cfg….
  tmpfreq(k) = ft_freqanalysis(cfg, tmpdata);

end

freq = tmpfreq(1);
freq.powspctrm = cat( 3-or-4-depending-on-whether-you-did-cfg.keeptrials=‘yes’-previously, tmpfreq.powspctrm);
freq.time = timepoint;
freq.dimord = (‘rpt_)chan_freq_time’;


Sounds like an overkill to me, though.

Best wishes, and good luck,

Jan-Mathijs

PS: Please feel free to suggest an update to the help-section of the ft_freqanalysis function, to explain better the cfg.pad parameter. We look forward to a PR!



On 24 Feb 2020, at 18:17, TORRALBA CUELLO, MIREIA <mireia.torralba at upf.edu<mailto:mireia.torralba at upf.edu>> wrote:

Hi,
I am a Fieldtrip user and I came across this error

ft_error('the specified padding is too short');

when calculating power spectrum using this code:

 cfg=[];
    cfg.method='mtmconvol';
    cfg.foi=2:1:40;
    cfg.t_ftimwin=0.5*ones(length(cfg.foi),1);
    cfg.pad=1;
cfg.taper='hanning';
fLast=ft_freqanalysis(cfg,dataLast);

As I see it, the padding should work in each of my time windows (0.5 seconds length each) and therefore the error should not appear, but when I inspected which is the segment padded by the function I saw
that what is being padded to 1 is the whole segment. I think this is not right, as what I would like is to increase my frequency resolution by padding each of the timewindows where I calculate the spectrum. The problem I have is that I want to use as a baseline another segment which has 0.5 seconds length, and as the frequency extracted by mtmconvol depends on the length of the segment, I am getting different frequency resolutions for the baseline and the target data.

Can anyone help me?
Thanks and best regards.

Mireia



Mireia Torralba Cuello
Multisensory Research Group
Center for Brain and Cognition, Universitat Pompeu Fabra
Address: Edifici Mercè Rodoreda 24.313
        c\ Ramon Trias Fargas, 25-27
        08005 Barcelona
http://www.mrg.upf.edu<http://www.mrg.upf.edu/>
Tel +34 935422745

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

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From jan.schoffelen at donders.ru.nl  Thu Feb 27 09:42:16 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 27 Feb 2020 08:42:16 +0000
Subject: [FieldTrip] Problem with Beamformer demo
In-Reply-To: <CANxafJ=attViuffT+a22T4AB_2_MOCb5kQC1gpyGZu6CLFFExQ@mail.gmail.com>
References: <CANxafJ=attViuffT+a22T4AB_2_MOCb5kQC1gpyGZu6CLFFExQ@mail.gmail.com>
Message-ID: <894A4A40-F4DB-4891-80C2-2922BC7FC488@donders.ru.nl>

Hi Zoltan,


Have you checked the values of the numbers in the functional data prior to calling ft_sourceinterpolate? This would give an indication of whether it is an interpolation issue or not.
I suspect that latter, because it seems that the interpolation is pulling ‘activity values’ into areas in the volume for which no functional estimate was provided.
This could happen if the specification of the ‘inside’ field in the source variable, prior to interpolation, behaves unpredictably.
Whether or not this is specific to the Matlab version used, I don’t know. Also, it is unclear what version of fieldtrip you are using.

What I can see in your script, though, is that the sourcePost_nocon you use to generate the first ‘correct’ 2 figures is loaded from disk, whereas the other source structure (with the ‘incorrect’ interpolation) is not.

Best wishes,
Jan-Mathijs


On 25 Feb 2020, at 13:46, Zoltan Juhasz <z65.juhasz at gmail.com<mailto:z65.juhasz at gmail.com>> wrote:

I have recently run into a problem while executing the Beamformer Fieldtrip demo at http://www.fieldtriptoolbox.org/tutorial/beamformer/

I am using the sample data set and the source code from this page but the picture I get for the section "Source Analysis: Contrast activity to another interval" is rather strange. I include here the 3 outputs, first two are correct, third one is the problematic one. Also included is the source. Matlab version used: R2019a. Could someone check whether it is a script error or perhaps a change in Matlab that generates the odd result?

links to figures and source:
https://drive.google.com/drive/folders/1XPZd5l3og1WAEt8dK6Bx7a9W8xgSzCMF?usp=sharing

Thanks,
Zoltan
University of Pannonia, Hungary
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

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From jan.schoffelen at donders.ru.nl  Thu Feb 27 09:58:27 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 27 Feb 2020 08:58:27 +0000
Subject: [FieldTrip] positions of Neuromag sensors rotated
In-Reply-To: <e9d298c450a441cb8fc51c054f268a8c@med.uni-duesseldorf.de>
References: <e9d298c450a441cb8fc51c054f268a8c@med.uni-duesseldorf.de>
Message-ID: <65A8AC04-6811-404A-B470-96893F76D805@donders.ru.nl>

Dear Jo,

Have you plotted the 2 headshapes in a single figure, and likewise for the gradiometers? In other words, which of the 4 objects is off in terms of expected location in space?
Have you checked for the problematic subject, whether the order of the landmark-clicking in the polhemus procedure was consistent with how the coordinate system is defined?

Best wishes,
JM

On 19 Feb 2020, at 15:15, joachim.lange at med.uni-duesseldorf.de<mailto:joachim.lange at med.uni-duesseldorf.de> wrote:

Dear Fieldtrippers,
I’m not sure whether my problem is a Fieldtrip or a Neuromag problem, but maybe someone can help me here.

I’ve recorded MEG data with a Neuromag system and the headshape and hpi coils using the polhemus system. When I read the headshape and the sensor locations from the fif-file and plot them using Fieldtrip, the plots look as expected, i.e., the “headshape” and the hpi coils are located within the MEG sensors / helmet (see attached example figures S1_1 and S1_2 from different angles). For one subject, however, the sensors from the hdr.grad-file seem rotated and it even looks like the “headshape” is partly outside the MEG sensors / helmet (see attached figures S2_1 and S2_2).
I have no idea what is going wrong here and/or how I could correct the apparently wrong positions. Any help would be much appreciated.
Thanks,
Jo

Ps: the simple FT-code:

hdr = ft_read_header(‘subject.fif’);
headshape = ft_read_headshape(‘subject.fif’);
figure;
ft_plot_sens(hdr.grad, 'style', 'b.', 'coil', 'false');
ft_plot_mesh(headshape.pos(1:4,:),'vertexsize',20,'vertexcolor','r'); %HPI coils
ft_plot_mesh(headshape.pos(5:end,:),'vertexsize',20,'vertexcolor','k'); %”manual” headshape
<S1_1.tif><S1_2.tif><S2_1.tif><S2_2.tif>_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

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From jan.schoffelen at donders.ru.nl  Thu Feb 27 10:25:17 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 27 Feb 2020 09:25:17 +0000
Subject: [FieldTrip] Possible bug in mtmconvol padding option
In-Reply-To: <65ACF498-3854-4EBD-AAA9-9BDFF4763AFD@donders.ru.nl>
References: <CALWZVf6kiji5FXt16MKKrL+T5SaYkH0N4mFRC4Tf-X8xTeU0Uw@mail.gmail.com>
 <65ACF498-3854-4EBD-AAA9-9BDFF4763AFD@donders.ru.nl>
Message-ID: <6E10027C-7D87-49CB-A159-72C16BBB1D4B@donders.ru.nl>

Hi Mireia,

There was a typo in my pseudo-code, the value to be used for cfg.pad would of course be 1.
Best,
JM


On 27 Feb 2020, at 09:29, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:

Hi Mireia,

Indeed the cfg.pad parameter operates on the full epoch length, not on the sliding window length. This is per design, and it is not a bug.

Although I don’t fully understand the deeper reason of why you want to do what you want to do, one way to get there would be to handcraft your own procedure, and create the TFRs in a computationally inefficient for-loop. This would require a lot of data bookkeeping on your end.

Procedurally:

for k = 1:the-number-of-time-point-onto-which-you-want-to-estimate-your-tfr

  cfg = [];
  cfg.latency = timepoint(k)+[-0.25 0.25-1./data.fsample];
  tmpdata = ft_selectdata(cfg, data);

  cfg = [];
  cfg.pad = 0.5;
  cfg.method = ‘mtmfft’;
  cfg….
  tmpfreq(k) = ft_freqanalysis(cfg, tmpdata);

end

freq = tmpfreq(1);
freq.powspctrm = cat( 3-or-4-depending-on-whether-you-did-cfg.keeptrials=‘yes’-previously, tmpfreq.powspctrm);
freq.time = timepoint;
freq.dimord = (‘rpt_)chan_freq_time’;


Sounds like an overkill to me, though.

Best wishes, and good luck,

Jan-Mathijs

PS: Please feel free to suggest an update to the help-section of the ft_freqanalysis function, to explain better the cfg.pad parameter. We look forward to a PR!



On 24 Feb 2020, at 18:17, TORRALBA CUELLO, MIREIA <mireia.torralba at upf.edu<mailto:mireia.torralba at upf.edu>> wrote:

Hi,
I am a Fieldtrip user and I came across this error

ft_error('the specified padding is too short');

when calculating power spectrum using this code:

 cfg=[];
    cfg.method='mtmconvol';
    cfg.foi=2:1:40;
    cfg.t_ftimwin=0.5*ones(length(cfg.foi),1);
    cfg.pad=1;
cfg.taper='hanning';
fLast=ft_freqanalysis(cfg,dataLast);

As I see it, the padding should work in each of my time windows (0.5 seconds length each) and therefore the error should not appear, but when I inspected which is the segment padded by the function I saw
that what is being padded to 1 is the whole segment. I think this is not right, as what I would like is to increase my frequency resolution by padding each of the timewindows where I calculate the spectrum. The problem I have is that I want to use as a baseline another segment which has 0.5 seconds length, and as the frequency extracted by mtmconvol depends on the length of the segment, I am getting different frequency resolutions for the baseline and the target data.

Can anyone help me?
Thanks and best regards.

Mireia



Mireia Torralba Cuello
Multisensory Research Group
Center for Brain and Cognition, Universitat Pompeu Fabra
Address: Edifici Mercè Rodoreda 24.313
        c\ Ramon Trias Fargas, 25-27
        08005 Barcelona
http://www.mrg.upf.edu<http://www.mrg.upf.edu/>
Tel +34 935422745

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

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From vaggelisstam at gmail.com  Thu Feb 27 13:11:31 2020
From: vaggelisstam at gmail.com (Vaggelis Stamkopoulos)
Date: Thu, 27 Feb 2020 14:11:31 +0200
Subject: [FieldTrip] Array forms to run statistics
Message-ID: <034FE493-8BD5-4E5D-AB0B-FB5AF0099189@gmail.com>

Greetings,

I have exported Time Frequency data from Brainstorm and the final power spectrum array is a 3D array t x s x f, where t = trials, s = samples, f = frequency. Is it in the right form to run statistics smoothly in Fieldtrip?

Thanks in advance,
Vaggelis


From jiaxiangzhang at gmail.com  Thu Feb 27 14:25:59 2020
From: jiaxiangzhang at gmail.com (Jiaxiang ZHANG)
Date: Thu, 27 Feb 2020 13:25:59 +0000
Subject: [FieldTrip] Research associate position at Cardiff University Brain
 Research Imaging Centre
In-Reply-To: <CANTmH_j3SRtGWY1fm9TdiUq7ii7RZ01pfcz=9+2Fo1aHsKN-Xw@mail.gmail.com>
References: <CANTmH_j3SRtGWY1fm9TdiUq7ii7RZ01pfcz=9+2Fo1aHsKN-Xw@mail.gmail.com>
Message-ID: <CANTmH_hrSgDfOo=7NDGXo8-j_cS8h9dar5cC3X8jwTqXYcEVMQ@mail.gmail.com>

[Apologize for cross-posting]

Dear all,

We are seeking an enthusiastic early-career scientist for a research
associate position at Cardiff University Brain Research Imaging Centre
(CUBRIC). The successful candidate will join a collaborative research team
to work on the neural mechanisms of human decision-making, integrating
multimodal brain imaging (MEG, functional MRI and diffusion MRI) and
computational modelling.

The successful candidate will design and conduct behavioural and brain
imaging experiments, in particular to take a lead role in integrating
imaging analysis from multiple modalities. The research aims to understand
the computational and neurocognitive processes of human decision-making,
and how individual differences in decision-making are influenced by
learning and brain stimulation. The research associate will also be
expected to collaborate with other researchers in the team on imaging data
analyses and data curation.

The research associate will have access to a unique combination of
state-of-the-art facilities and world-leading expertise at CUBRIC, with 4
human MRI systems (2 x Siemens Prisma, 1 x Siemens Connectom, 1 x Siemens
7T), MEG, EEG, TMS, tDCS, clinical research units and testing labs. Further
details of CUBRIC can be found on our webpage (
http://sites.cardiff.ac.uk/cubric).

This is a full-time, fixed-term position available from now until February
2022. For informal enquiries, please contact Dr Jiaxiang Zhang (
zhangj73 at cardiff.ac.uk). A formal application needs to be submitted via the
link online (https://www.jobs.ac.uk/job/BYT794/research-associate).
Application deadline: March 18th, 2020.

------

Dr. Jiaxiang Zhang
Cardiff University Brain Research Imaging Centre (CUBRIC)
School of Psychology
Cardiff University
Maindy Road, Cardiff, CF24 4HQ
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From rjhubba2 at illinois.edu  Thu Feb 27 21:22:28 2020
From: rjhubba2 at illinois.edu (Ryan Hubbard)
Date: Thu, 27 Feb 2020 14:22:28 -0600
Subject: [FieldTrip] 'avgoverchan' doesn't seem to do anything
Message-ID: <CAM7AsA9yHsVE2okLv8fYdJo_OW5g=-oOpj5tB+MvEjxnF8pMAA@mail.gmail.com>

Hi all,
I'm having an issue running cluster analyses on some data I have. Following
this thread here (
https://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006853.html),
it seems like I should be able to specify 'avgoverchan' in my cfg, and then
when I run a cluster analysis, it won't consider spatial information. In
fact, looking at ft_statistics_montecarlo, I see a section that states:

  elseif isfield(cfg, 'avgoverchan') && istrue(cfg.avgoverchan)
      % channel dimension has been averaged across, no sense in clustering
across space
      cfg.connectivity = true(1);

However, once we reach the "clusterstat" function this appears to be
completely disregarded, and it searches for spatial information. I don't
even see anything that reads the "connectivity" from the cfg in that
function. I then get an error that states 'invalid dimension of
spatdimneighbstructmat', as it is trying to look for channel neighbors to
form clusters. This is true for both timelockstatistics and freqstatistics
(as they both call ft_statistics_montecarlo).

This is unfortunate, because it would be good to apply these cluster
analysis functions to other time-series data (e.g. classification
accuracies across time) where there aren't channels, but temporal
clustering would still be useful. Can anyone help me with this?

Thanks,
Ryan

-- 
Ryan Hubbard
Beckman Postdoctoral Fellow
The Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
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From swain083 at uottawa.ca  Thu Feb 27 22:00:57 2020
From: swain083 at uottawa.ca (Soren Emmanuel Wainio-Theberge)
Date: Thu, 27 Feb 2020 16:00:57 -0500
Subject: [FieldTrip] eLORETA spatial filter issues
Message-ID: <CAEh-AjwLJ8BjNaquAOvvLavCBqsZnSCgeKN8dzRCfbOD7Sibzw@mail.gmail.com>

Hello Fieldtrip community,

I am a student researcher at the University of Ottawa in the Mind, Brain
Imaging, and Neuroethics unit. I have been trying to do source-space
analysis on the Human Connectome Project MEG dataset and I had some
questions about getting virtual channels using the eLORETA method. I have
been following the tutorial here (
http://www.fieldtriptoolbox.org/tutorial/virtual_sensors/) which describes
this process for LCMV beamformers.

However, when looking at the code of ft_eloreta and doing some tests of my
own, I found that the spatial filter that I get from the eLORETA method
doesn't depend on the data - that is, if I take two subjects with the same
channels, leadfield and headmodel (but different data), the spatial filter
I get from source analysis is the same for each subject. This doesn't
happen if I use other source analysis methods, such as minimum norm
estimation.

My two questions are:
1) Should the filter really be independent of the data like this? Is this
just a difference between the two methods (eLORETA and MNE)?
2) If the independence of the filter is due to a difference between the
methods, is eLORETA suitable for the extraction of virtual channels in the
same way as described in the tutorial linked above?

Any help would be very much appreciated.

Best and thanks very much in advance,
Soren
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From e.spaak at donders.ru.nl  Fri Feb 28 09:11:08 2020
From: e.spaak at donders.ru.nl (Eelke Spaak)
Date: Fri, 28 Feb 2020 09:11:08 +0100
Subject: [FieldTrip] 'avgoverchan' doesn't seem to do anything
In-Reply-To: <CAM7AsA9yHsVE2okLv8fYdJo_OW5g=-oOpj5tB+MvEjxnF8pMAA@mail.gmail.com>
References: <CAM7AsA9yHsVE2okLv8fYdJo_OW5g=-oOpj5tB+MvEjxnF8pMAA@mail.gmail.com>
Message-ID: <CABPNLUoc04YNzYi47h5NvoavNUk+JQQ3ns=ZuVRtQPe+yFZq6w@mail.gmail.com>

Hi Ryan,

Are you using ft_statistics_montecarlo directly? Or using one of the
high-level stats functions (e.g. ft_timelockstatistics, etc.)? It's
usually easier to use the latter, since they keep track of bookkeeping
stuff like averaging the data over various dimensions.

If you are using a high-level interface, have you tried specifying
cfg.neighbours = []?

Good luck,
Eelke

On Thu, 27 Feb 2020 at 21:22, Ryan Hubbard <rjhubba2 at illinois.edu> wrote:
>
> Hi all,
> I'm having an issue running cluster analyses on some data I have. Following this thread here (https://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006853.html), it seems like I should be able to specify 'avgoverchan' in my cfg, and then when I run a cluster analysis, it won't consider spatial information. In fact, looking at ft_statistics_montecarlo, I see a section that states:
>
>   elseif isfield(cfg, 'avgoverchan') && istrue(cfg.avgoverchan)
>       % channel dimension has been averaged across, no sense in clustering across space
>       cfg.connectivity = true(1);
>
> However, once we reach the "clusterstat" function this appears to be completely disregarded, and it searches for spatial information. I don't even see anything that reads the "connectivity" from the cfg in that function. I then get an error that states 'invalid dimension of spatdimneighbstructmat', as it is trying to look for channel neighbors to form clusters. This is true for both timelockstatistics and freqstatistics (as they both call ft_statistics_montecarlo).
>
> This is unfortunate, because it would be good to apply these cluster analysis functions to other time-series data (e.g. classification accuracies across time) where there aren't channels, but temporal clustering would still be useful. Can anyone help me with this?
>
> Thanks,
> Ryan
>
> --
> Ryan Hubbard
> Beckman Postdoctoral Fellow
> The Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202



From Joachim.Lange at med.uni-duesseldorf.de  Fri Feb 28 09:41:56 2020
From: Joachim.Lange at med.uni-duesseldorf.de (Joachim.Lange at med.uni-duesseldorf.de)
Date: Fri, 28 Feb 2020 08:41:56 +0000
Subject: [FieldTrip] positions of Neuromag sensors rotated
Message-ID: <47bfa413ad3743fd843a1270548f3c21@med.uni-duesseldorf.de>

Dear JM ;)
Thanks for your reply and the suggestions. I had done the plotting you suggested and it's the MEG sensors of the problematic subject that are off. I also had a second look at the landmarks (and the other polhemus recordings in the "headshape" variable) but couldn't find anything suspicious.
Best,
Jo


> Date: Thu, 27 Feb 2020 08:58:27 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] positions of Neuromag sensors rotated
> Message-ID: <65A8AC04-6811-404A-B470-96893F76D805 at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Jo,
> 
> Have you plotted the 2 headshapes in a single figure, and likewise for the
> gradiometers? In other words, which of the 4 objects is off in terms of
> expected location in space?
> Have you checked for the problematic subject, whether the order of the
> landmark-clicking in the polhemus procedure was consistent with how the
> coordinate system is defined?
> 
> Best wishes,
> JM
> 
> On 19 Feb 2020, at 15:15, joachim.lange at med.uni-
> duesseldorf.de<mailto:joachim.lange at med.uni-duesseldorf.de> wrote:
> 
> Dear Fieldtrippers,
> I’m not sure whether my problem is a Fieldtrip or a Neuromag problem, but
> maybe someone can help me here.
> 
> I’ve recorded MEG data with a Neuromag system and the headshape and hpi
> coils using the polhemus system. When I read the headshape and the sensor
> locations from the fif-file and plot them using Fieldtrip, the plots look as
> expected, i.e., the “headshape” and the hpi coils are located within the MEG
> sensors / helmet (see attached example figures S1_1 and S1_2 from
> different angles). For one subject, however, the sensors from the hdr.grad-
> file seem rotated and it even looks like the “headshape” is partly outside the
> MEG sensors / helmet (see attached figures S2_1 and S2_2).
> I have no idea what is going wrong here and/or how I could correct the
> apparently wrong positions. Any help would be much appreciated.
> Thanks,
> Jo
> 
> Ps: the simple FT-code:
> 
> hdr = ft_read_header(‘subject.fif’);
> headshape = ft_read_headshape(‘subject.fif’);
> figure;
> ft_plot_sens(hdr.grad, 'style', 'b.', 'coil', 'false');
> ft_plot_mesh(headshape.pos(1:4,:),'vertexsize',20,'vertexcolor','r'); %HPI
> coils
> ft_plot_mesh(headshape.pos(5:end,:),'vertexsize',20,'vertexcolor','k');
> %”manual” headshape
> <S1_1.tif><S1_2.tif><S2_1.tif><S2_2.tif>___________________________
> ____________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200227/e4
> 8fc5ac/attachment-0001.htm>
> 
> ------------------------------
> 
> Message: 6
> Date: Thu, 27 Feb 2020 09:25:17 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Possible bug in mtmconvol padding option
> Message-ID: <6E10027C-7D87-49CB-A159-72C16BBB1D4B at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Mireia,
> 
> There was a typo in my pseudo-code, the value to be used for cfg.pad would
> of course be 1.
> Best,
> JM
> 
> 
> On 27 Feb 2020, at 09:29, Schoffelen, J.M. (Jan Mathijs)
> <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>>
> wrote:
> 
> Hi Mireia,
> 
> Indeed the cfg.pad parameter operates on the full epoch length, not on the
> sliding window length. This is per design, and it is not a bug.
> 
> Although I don’t fully understand the deeper reason of why you want to do
> what you want to do, one way to get there would be to handcraft your own
> procedure, and create the TFRs in a computationally inefficient for-loop. This
> would require a lot of data bookkeeping on your end.
> 
> Procedurally:
> 
> for k = 1:the-number-of-time-point-onto-which-you-want-to-estimate-your-
> tfr
> 
>   cfg = [];
>   cfg.latency = timepoint(k)+[-0.25 0.25-1./data.fsample];
>   tmpdata = ft_selectdata(cfg, data);
> 
>   cfg = [];
>   cfg.pad = 0.5;
>   cfg.method = ‘mtmfft’;
>   cfg….
>   tmpfreq(k) = ft_freqanalysis(cfg, tmpdata);
> 
> end
> 
> freq = tmpfreq(1);
> freq.powspctrm = cat( 3-or-4-depending-on-whether-you-did-
> cfg.keeptrials=‘yes’-previously, tmpfreq.powspctrm);
> freq.time = timepoint;
> freq.dimord = (‘rpt_)chan_freq_time’;
> 
> 
> Sounds like an overkill to me, though.
> 
> Best wishes, and good luck,
> 
> Jan-Mathijs
> 
> PS: Please feel free to suggest an update to the help-section of the
> ft_freqanalysis function, to explain better the cfg.pad parameter. We look
> forward to a PR!
> 
> 
> 
> On 24 Feb 2020, at 18:17, TORRALBA CUELLO, MIREIA
> <mireia.torralba at upf.edu<mailto:mireia.torralba at upf.edu>> wrote:
> 
> Hi,
> I am a Fieldtrip user and I came across this error
> 
> ft_error('the specified padding is too short');
> 
> when calculating power spectrum using this code:
> 
>  cfg=[];
>     cfg.method='mtmconvol';
>     cfg.foi=2:1:40;
>     cfg.t_ftimwin=0.5*ones(length(cfg.foi),1);
>     cfg.pad=1;
> cfg.taper='hanning';
> fLast=ft_freqanalysis(cfg,dataLast);
> 
> As I see it, the padding should work in each of my time windows (0.5 seconds
> length each) and therefore the error should not appear, but when I
> inspected which is the segment padded by the function I saw
> that what is being padded to 1 is the whole segment. I think this is not right,
> as what I would like is to increase my frequency resolution by padding each
> of the timewindows where I calculate the spectrum. The problem I have is
> that I want to use as a baseline another segment which has 0.5 seconds
> length, and as the frequency extracted by mtmconvol depends on the length
> of the segment, I am getting different frequency resolutions for the baseline
> and the target data.
> 
> Can anyone help me?
> Thanks and best regards.
> 
> Mireia
> 
> 
> 
> Mireia Torralba Cuello
> Multisensory Research Group
> Center for Brain and Cognition, Universitat Pompeu Fabra
> Address: Edifici Mercè Rodoreda 24.313
>         c\ Ramon Trias Fargas, 25-27
>         08005 Barcelona
> http://www.mrg.upf.edu<http://www.mrg.upf.edu/>
> Tel +34 935422745
> 
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
> 
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
> 
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> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
> 
> 
> ------------------------------
> 
> End of fieldtrip Digest, Vol 111, Issue 21
> ******************************************



From jan.schoffelen at donders.ru.nl  Fri Feb 28 10:18:32 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 28 Feb 2020 09:18:32 +0000
Subject: [FieldTrip] positions of Neuromag sensors rotated
In-Reply-To: <47bfa413ad3743fd843a1270548f3c21@med.uni-duesseldorf.de>
References: <47bfa413ad3743fd843a1270548f3c21@med.uni-duesseldorf.de>
Message-ID: <91D47250-8461-48E9-A60A-02E2E5F3C93B@donders.ru.nl>

Hi Jo,
Is there another way in which you can check the  coregistration information in the fif-file? E.g. in the Elekta,  apologies, Megin software? If I recall well, but I am no expert here, there may be various coordinate systems defined in the fif-files, and it could be that something went wrong there.

Best wishes,
JM


On 28 Feb 2020, at 09:41, joachim.lange at med.uni-duesseldorf.de<mailto:joachim.lange at med.uni-duesseldorf.de> wrote:

Dear JM ;)
Thanks for your reply and the suggestions. I had done the plotting you suggested and it's the MEG sensors of the problematic subject that are off. I also had a second look at the landmarks (and the other polhemus recordings in the "headshape" variable) but couldn't find anything suspicious.
Best,
Jo


Date: Thu, 27 Feb 2020 08:58:27 +0000
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>>
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] positions of Neuromag sensors rotated
Message-ID: <65A8AC04-6811-404A-B470-96893F76D805 at donders.ru.nl<mailto:65A8AC04-6811-404A-B470-96893F76D805 at donders.ru.nl>>
Content-Type: text/plain; charset="utf-8"

Dear Jo,

Have you plotted the 2 headshapes in a single figure, and likewise for the
gradiometers? In other words, which of the 4 objects is off in terms of
expected location in space?
Have you checked for the problematic subject, whether the order of the
landmark-clicking in the polhemus procedure was consistent with how the
coordinate system is defined?

Best wishes,
JM

On 19 Feb 2020, at 15:15, joachim.lange at med.uni<mailto:joachim.lange at med.uni>-
duesseldorf.de<http://duesseldorf.de><mailto:joachim.lange at med.uni-duesseldorf.de> wrote:

Dear Fieldtrippers,
I’m not sure whether my problem is a Fieldtrip or a Neuromag problem, but
maybe someone can help me here.

I’ve recorded MEG data with a Neuromag system and the headshape and hpi
coils using the polhemus system. When I read the headshape and the sensor
locations from the fif-file and plot them using Fieldtrip, the plots look as
expected, i.e., the “headshape” and the hpi coils are located within the MEG
sensors / helmet (see attached example figures S1_1 and S1_2 from
different angles). For one subject, however, the sensors from the hdr.grad-
file seem rotated and it even looks like the “headshape” is partly outside the
MEG sensors / helmet (see attached figures S2_1 and S2_2).
I have no idea what is going wrong here and/or how I could correct the
apparently wrong positions. Any help would be much appreciated.
Thanks,
Jo

Ps: the simple FT-code:

hdr = ft_read_header(‘subject.fif’);
headshape = ft_read_headshape(‘subject.fif’);
figure;
ft_plot_sens(hdr.grad, 'style', 'b.', 'coil', 'false');
ft_plot_mesh(headshape.pos(1:4,:),'vertexsize',20,'vertexcolor','r'); %HPI
coils
ft_plot_mesh(headshape.pos(5:end,:),'vertexsize',20,'vertexcolor','k');
%”manual” headshape
<S1_1.tif><S1_2.tif><S2_1.tif><S2_2.tif>___________________________
____________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

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------------------------------

Message: 6
Date: Thu, 27 Feb 2020 09:25:17 +0000
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Possible bug in mtmconvol padding option
Message-ID: <6E10027C-7D87-49CB-A159-72C16BBB1D4B at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"

Hi Mireia,

There was a typo in my pseudo-code, the value to be used for cfg.pad would
of course be 1.
Best,
JM


On 27 Feb 2020, at 09:29, Schoffelen, J.M. (Jan Mathijs)
<jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>>
wrote:

Hi Mireia,

Indeed the cfg.pad parameter operates on the full epoch length, not on the
sliding window length. This is per design, and it is not a bug.

Although I don’t fully understand the deeper reason of why you want to do
what you want to do, one way to get there would be to handcraft your own
procedure, and create the TFRs in a computationally inefficient for-loop. This
would require a lot of data bookkeeping on your end.

Procedurally:

for k = 1:the-number-of-time-point-onto-which-you-want-to-estimate-your-
tfr

 cfg = [];
 cfg.latency = timepoint(k)+[-0.25 0.25-1./data.fsample];
 tmpdata = ft_selectdata(cfg, data);

 cfg = [];
 cfg.pad = 0.5;
 cfg.method = ‘mtmfft’;
 cfg….
 tmpfreq(k) = ft_freqanalysis(cfg, tmpdata);

end

freq = tmpfreq(1);
freq.powspctrm = cat( 3-or-4-depending-on-whether-you-did-
cfg.keeptrials=‘yes’-previously, tmpfreq.powspctrm);
freq.time = timepoint;
freq.dimord = (‘rpt_)chan_freq_time’;


Sounds like an overkill to me, though.

Best wishes, and good luck,

Jan-Mathijs

PS: Please feel free to suggest an update to the help-section of the
ft_freqanalysis function, to explain better the cfg.pad parameter. We look
forward to a PR!



On 24 Feb 2020, at 18:17, TORRALBA CUELLO, MIREIA
<mireia.torralba at upf.edu<mailto:mireia.torralba at upf.edu>> wrote:

Hi,
I am a Fieldtrip user and I came across this error

ft_error('the specified padding is too short');

when calculating power spectrum using this code:

cfg=[];
   cfg.method='mtmconvol';
   cfg.foi=2:1:40;
   cfg.t_ftimwin=0.5*ones(length(cfg.foi),1);
   cfg.pad=1;
cfg.taper='hanning';
fLast=ft_freqanalysis(cfg,dataLast);

As I see it, the padding should work in each of my time windows (0.5 seconds
length each) and therefore the error should not appear, but when I
inspected which is the segment padded by the function I saw
that what is being padded to 1 is the whole segment. I think this is not right,
as what I would like is to increase my frequency resolution by padding each
of the timewindows where I calculate the spectrum. The problem I have is
that I want to use as a baseline another segment which has 0.5 seconds
length, and as the frequency extracted by mtmconvol depends on the length
of the segment, I am getting different frequency resolutions for the baseline
and the target data.

Can anyone help me?
Thanks and best regards.

Mireia



Mireia Torralba Cuello
Multisensory Research Group
Center for Brain and Cognition, Universitat Pompeu Fabra
Address: Edifici Mercè Rodoreda 24.313
       c\ Ramon Trias Fargas, 25-27
       08005 Barcelona
http://www.mrg.upf.edu<http://www.mrg.upf.edu/>
Tel +34 935422745

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From jan.schoffelen at donders.ru.nl  Fri Feb 28 13:20:21 2020
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 28 Feb 2020 12:20:21 +0000
Subject: [FieldTrip] eLORETA spatial filter issues
In-Reply-To: <CAEh-AjwLJ8BjNaquAOvvLavCBqsZnSCgeKN8dzRCfbOD7Sibzw@mail.gmail.com>
References: <CAEh-AjwLJ8BjNaquAOvvLavCBqsZnSCgeKN8dzRCfbOD7Sibzw@mail.gmail.com>
Message-ID: <A152A645-5B8F-469B-A25C-69F4A5B25F34@donders.ru.nl>

Hi Soren,

Just to clarify, if with ‘data dependent’, you mean ‘electrophysiological data dependent’. The reason I mention this, is that clearly one should consider using subject-specific headmodels and leadfields if possible (and with the HCP MEG data this is definitely possible), which will result in different spatial filters for different subjects.

But indeed, it depends on the inverse algorithm whether or not the spatial filter is a function of the leadfields only (e.g. eLORETA), or whether some aspect of the data is taken into account (MNE: noise covariance (optional), beamformers: data covariance).

So:

> My two questions are: 
> 1) Should the filter really be independent of the data like this? Is this just a difference between the two methods (eLORETA and MNE)? 

Yes, and Yes.

> 2) If the independence of the filter is due to a difference between the methods, is eLORETA suitable for the extraction of virtual channels in the same way as described in the tutorial linked above? 

Well, the fact that the eLORETA spatial filter is merely a function of the leadfield (+some additional spatial smoothness constraints), this does not invalidate it to be used as a spatial filter, although I’d rather use a technique (beamformer, or if I have to: MNE) which is a bit more to the spatial point.

Best wishes,
Jan-Mathijs


> 
> Any help would be very much appreciated. 
> 
> Best and thanks very much in advance, 
> Soren
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202




From jiversen at ucsd.edu  Fri Feb 28 23:12:22 2020
From: jiversen at ucsd.edu (Iversen, John)
Date: Fri, 28 Feb 2020 22:12:22 +0000
Subject: [FieldTrip] Reminder: 4th International MoBI conference abstract
 deadline is in one week!
In-Reply-To: <24CFB669-8D48-4A57-9EE1-1E43DD1055A3@ucsd.edu>
References: <24CFB669-8D48-4A57-9EE1-1E43DD1055A3@ucsd.edu>
Message-ID: <AE23F7F6-F181-41A5-86FD-7BCE57FD12D0@ucsd.edu>

Dear MoBI fans, colleagues, and friends,

We hope you will join us San Diego for the 4TH INTERNATIONAL MOBILE BRAIN/BODY IMAGING (MoBI) CONFERENCE, which will take place June 7-10, 2020 at the University of California San Diego hosted by the Swartz Center for Computational Neuroscience. Reminder: abstract submission deadline is next Friday, March 6th: http://mobi2020.ucsd.edu<http://mobi2020.ucsd.edu/>. Please circulate this announcement to colleagues and trainees. Students and Postdoctoral fellows are especially invited to apply, with discounted registration.


We'd also like to let you know about two associated events bookending the MoBI conference that will be of interest:
June 7: 2nd Hands-on Lab Streaming Layer workshop (https://sites.google.com/ucsd.edu/eeglab2020/lsl-workshop-2020).
June 11: NSF Group Brain Dynamics Workshop: For anyone studying interpersonal interactions (or hoping to), we will have a day-long workshop with leading practitioners from around the world to share the state of the art in multi-person brain/body recording and analysis, and solve existing challenges. (https://sites.google.com/ucsd.edu/mobi2020/group-brain-dyn-workshop)
(In addition, the prior week will be a full EEGLAB workshop: http://eeglab2020.ucsd.edu<http://eeglab2020.ucsd.edu/>)


MoBI Conference Details

Mobile Brain/Body Imaging (MoBI) is a new imaging approach employing mobile brain imaging methods synchronized to body motion capture and other behavioral and psychophysiological data streams to investigate brain dynamics accompanying natural cognitive and affective processes as humans interact with their environment and/or with others. Join MoBI researchers from around the world for three stimulating Keynotes by Stefan Debener (Benefits and pitfalls of wearable EEG), Laurel Trainor (Rhythm, prediction and multi-person interaction in music), and Sarah Robinson (Extended Organisms/Surrogate Bodies). Oral sessions will include the latest developments in imaging hardware, new software solutions to record and analyze multi-modal data streams, and MoBI applications in a wide range of research areas including spatial cognition, motor control, gait rehabilitation, sport science, music and dance, therapeutic interventions and others.

Abstract submission is now open (Deadline March 6, 2020) and discounted Early-Bird Registration is available through April 1st. Full conference information can be found at http://mobi2020.ucsd.edu<http://mobi2020.ucsd.edu/>. In case you have questions or comments please contact conference co-organizer John Iversen (jiversen at ucsd.edu<mailto:jiversen at ucsd.edu>).

Best,

John Iversen
Klaus Gramann

--
John R. Iversen, PhD
University of California, San Diego
Associate Director, Swartz Center for Computational Neuroscience
Institute for Neural Computation
9500 Gilman Dr #0559
La Jolla, CA 92093
jiversen at ucsd.edu<mailto:jiversen at ucsd.edu>

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